1-26602511-T-G

Variant names:

• chr1-26602511-T-G
• rs17162257
• ENST00000516620.2:n.-79A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067342.1(LOC124904769):​n.-79A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,114 control chromosomes in the GnomAD database, including 7,614 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.21 (7614 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC124904769 XR_007067342.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 8 publications found

Genes affected

RNU7-29P (HGNC:34125): (RNA, U7 small nuclear 29 pseudogene)

LOC124904769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000516620.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNU7-29P	ENST00000516620.2	TSL:6	n.-79A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31447 AN: 151996 Hom.: 7576 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.164

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31547 AN: 152114 Hom.: 7614 Cov.: 32 AF XY: 0.204 AC XY: 15200 AN XY: 74392

African (AFR) AF: 0.579 AC: 23979 AN: 41438

American (AMR) AF: 0.230 AC: 3507 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3462

East Asian (EAS) AF: 0.111 AC: 574 AN: 5168

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4828

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0358 AC: 2434 AN: 68010

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.0883 Hom.: 8509

Bravo AF: 0.241

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs17162257; hg19: chr1-26929002;