chr1-161499264-G-C

Variant names:

• chr1-161499264-G-C
• rs6658353

Variant summary

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

The variant allele was found at a frequency of 0.491 in 151,780 control chromosomes in the GnomAD database, including 18,697 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 0.49 (18697 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74432 AN: 151662 Hom.: 18696 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.491 AC: 74474 AN: 151780 Hom.: 18697 Cov.: 31 AF XY: 0.486 AC XY: 36080 AN XY: 74174

African (AFR) AF: 0.529 AC: 21849 AN: 41340

American (AMR) AF: 0.433 AC: 6605 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5170

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4808

European-Finnish (FIN) AF: 0.502 AC: 5290 AN: 10528

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34553 AN: 67900

Other (OTH) AF: 0.481 AC: 1012 AN: 2106

Alfa AF: 0.352 Hom.: 877

Bravo AF: 0.491

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6658353; hg19: chr1-161469054;