rs1609772

Variant names:

• chr1-188584468-C-A
• rs1609772

Your query was ambiguous. Multiple possible variants found:

• chr1-188584468-C-A
• chr1-188584468-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.254 in 152,052 control chromosomes in the GnomAD database, including 4,986 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 0.25 (4986 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 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: 0.254 AC: 38560 AN: 151934 Hom.: 4977 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.254 AC: 38581 AN: 152052 Hom.: 4986 Cov.: 33 AF XY: 0.253 AC XY: 18809 AN XY: 74316

African (AFR) AF: 0.239 AC: 9928 AN: 41486

American (AMR) AF: 0.200 AC: 3047 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1364 AN: 5152

South Asian (SAS) AF: 0.402 AC: 1933 AN: 4814

European-Finnish (FIN) AF: 0.261 AC: 2766 AN: 10594

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17722 AN: 67964

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.256 Hom.: 16137

Bravo AF: 0.243

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1609772; hg19: chr1-188553599;