rs71628639

Variant names:

• chr1-155015779-C-A
• rs71628639
• NM_001256455.2:c.1119C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-155015779-C-A
• chr1-155015779-C-T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_001256455.2(ZBTB7B):​c.1119C>A​(p.Pro373Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,612,224 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (27 hom., cov: 33)
  • Exomes 𝑓: 0.012 (174 hom.)
• Consequence: ZBTB7B NM_001256455.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0500
• Publications: 6 publications found

Genes affected

ZBTB7B (HGNC:18668): (zinc finger and BTB domain containing 7B) This gene encodes a zinc finger-containing transcription factor that acts as a key regulator of lineage commitment of immature T-cell precursors. It is necessary and sufficient for commitment of CD4 lineage, while its absence causes CD8 commitment. It also functions as a transcriptional repressor of type I collagen genes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP6: Variant 1-155015779-C-A is Benign according to our data. Variant chr1-155015779-C-A is described in ClinVar as Benign. ClinVar VariationId is 713771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.05 with no splicing effect.
• BS2: High AC in GnomAd4 at 1645 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256455.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB7B	NM_001256455.2	MANE Select	c.1119C>A	p.Pro373Pro	synonymous	Exon 2 of 3	NP_001243384.1	O15156-1
	ZBTB7B	NM_001252406.3		c.1221C>A	p.Pro407Pro	synonymous	Exon 4 of 5	NP_001239335.1	O15156-2
	ZBTB7B	NM_001377451.1		c.1221C>A	p.Pro407Pro	synonymous	Exon 5 of 6	NP_001364380.1	O15156-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB7B	ENST00000535420.6	TSL:5 MANE Select	c.1119C>A	p.Pro373Pro	synonymous	Exon 2 of 3	ENSP00000438647.1	O15156-1
	ZBTB7B	ENST00000292176.2	TSL:1	c.1119C>A	p.Pro373Pro	synonymous	Exon 1 of 2	ENSP00000292176.2	O15156-1
	ZBTB7B	ENST00000368426.3	TSL:1	c.1119C>A	p.Pro373Pro	synonymous	Exon 3 of 4	ENSP00000357411.3	O15156-1

Frequencies

GnomAD3 genomes AF: 0.0108 AC: 1646 AN: 152236 Hom.: 27 Cov.: 33

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00680

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.00955

GnomAD2 exomes AF: 0.0107 AC: 2681 AN: 249400 AF XY: 0.0106

Gnomad AFR exome AF: 0.00172

Gnomad AMR exome AF: 0.00374

Gnomad ASJ exome AF: 0.00419

Gnomad EAS exome AF: 0.0000551

Gnomad FIN exome AF: 0.0473

Gnomad NFE exome AF: 0.0117

Gnomad OTH exome AF: 0.0102

GnomAD4 exome AF: 0.0123 AC: 17921 AN: 1459870 Hom.: 174 Cov.: 35 AF XY: 0.0118 AC XY: 8599 AN XY: 726248

African (AFR) AF: 0.00183 AC: 61 AN: 33412

American (AMR) AF: 0.00367 AC: 164 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.00394 AC: 103 AN: 26128

East Asian (EAS) AF: 0.0000504 AC: 2 AN: 39700

South Asian (SAS) AF: 0.00217 AC: 187 AN: 86164

European-Finnish (FIN) AF: 0.0461 AC: 2464 AN: 53394

Middle Eastern (MID) AF: 0.00118 AC: 5 AN: 4254

European-Non Finnish (NFE) AF: 0.0130 AC: 14406 AN: 1111894

Other (OTH) AF: 0.00879 AC: 529 AN: 60216

GnomAD4 genome AF: 0.0108 AC: 1645 AN: 152354 Hom.: 27 Cov.: 33 AF XY: 0.0123 AC XY: 918 AN XY: 74506

African (AFR) AF: 0.00255 AC: 106 AN: 41594

American (AMR) AF: 0.00679 AC: 104 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4830

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0124 AC: 841 AN: 68024

Other (OTH) AF: 0.00945 AC: 20 AN: 2116

Alfa AF: 0.0115 Hom.: 18

Bravo AF: 0.00694

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00872

EpiControl AF: 0.00984

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	9.4
DANN	Benign	0.83
PhyloP100		-0.050
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs71628639; hg19: chr1-154988255; COSMIC: COSV99421736; COSMIC: COSV99421736;