chr7-73537310-C-G

Variant names:

• chr7-73537310-C-G
• rs142166738
• NM_001707.4:c.597G>C

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001707.4(BCL7B):​c.597G>C​(p.Ala199Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0036 in 1,614,024 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0037 (18 hom.)
• Consequence: BCL7B NM_001707.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.81
• Publications: 4 publications found

Genes affected

BCL7B (HGNC:1005): (BAF chromatin remodeling complex subunit BCL7B) This gene encodes a member of the BCL7 family including BCL7A, BCL7B and BCL7C proteins. This member is BCL7B, which contains a region that is highly similar to the N-terminal segment of BCL7A or BCL7C proteins. The BCL7A protein is encoded by the gene known to be directly involved in a three-way gene translocation in a Burkitt lymphoma cell line. This gene is located at a chromosomal region commonly deleted in Williams syndrome. This gene is highly conserved from C. elegans to human. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 7-73537310-C-G is Benign according to our data. Variant chr7-73537310-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2657554.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.81 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 18 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001707.4. 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
	BCL7B	NM_001707.4	MANE Select	c.597G>C	p.Ala199Ala	synonymous	Exon 6 of 6	NP_001698.2
	BCL7B	NM_001301061.2		c.630G>C	p.Ala210Ala	synonymous	Exon 7 of 7	NP_001287990.1	F2Z3H6
	BCL7B	NM_001197244.2		c.426G>C	p.Ala142Ala	synonymous	Exon 5 of 5	NP_001184173.1	Q9BQE9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL7B	ENST00000223368.7	TSL:1 MANE Select	c.597G>C	p.Ala199Ala	synonymous	Exon 6 of 6	ENSP00000223368.2	Q9BQE9-1
	BCL7B	ENST00000945444.1		c.708G>C	p.Ala236Ala	synonymous	Exon 7 of 7	ENSP00000615503.1
	BCL7B	ENST00000871802.1		c.675G>C	p.Ala225Ala	synonymous	Exon 7 of 7	ENSP00000541861.1

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 351 AN: 152164 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.00527

GnomAD2 exomes AF: 0.00289 AC: 724 AN: 250442 AF XY: 0.00287

Gnomad AFR exome AF: 0.000431

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.0144

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00319

Gnomad NFE exome AF: 0.00346

Gnomad OTH exome AF: 0.00425

GnomAD4 exome AF: 0.00373 AC: 5459 AN: 1461742 Hom.: 18 Cov.: 31 AF XY: 0.00375 AC XY: 2725 AN XY: 727174

African (AFR) AF: 0.000538 AC: 18 AN: 33478

American (AMR) AF: 0.00134 AC: 60 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.0152 AC: 397 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.00141 AC: 122 AN: 86252

European-Finnish (FIN) AF: 0.00275 AC: 147 AN: 53392

Middle Eastern (MID) AF: 0.00833 AC: 48 AN: 5764

European-Non Finnish (NFE) AF: 0.00398 AC: 4429 AN: 1111930

Other (OTH) AF: 0.00394 AC: 238 AN: 60380

GnomAD4 genome AF: 0.00230 AC: 350 AN: 152282 Hom.: 0 Cov.: 32 AF XY: 0.00203 AC XY: 151 AN XY: 74472

African (AFR) AF: 0.000625 AC: 26 AN: 41568

American (AMR) AF: 0.00105 AC: 16 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00124 AC: 6 AN: 4826

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10624

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00321 AC: 218 AN: 68014

Other (OTH) AF: 0.00521 AC: 11 AN: 2110

Alfa AF: 0.00281 Hom.: 0

Bravo AF: 0.00214

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00333

EpiControl AF: 0.00456

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.018
DANN	Benign	0.51
PhyloP100		-2.8
Mutation Taster		=99/1	polymorphism

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: rs142166738; hg19: chr7-72951640;