rs660975

Variant names:

• chr1-209827703-A-C
• rs660975

Your query was ambiguous. Multiple possible variants found:

• chr1-209827703-A-C
• chr1-209827703-A-T

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 0.52 in 151,242 control chromosomes in the GnomAD database, including 21,006 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 0.52 (21006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 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: 0.520 AC: 78553 AN: 151128 Hom.: 20998 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.520 AC: 78593 AN: 151242 Hom.: 21006 Cov.: 32 AF XY: 0.512 AC XY: 37844 AN XY: 73954

African (AFR) AF: 0.526 AC: 21448 AN: 40762

American (AMR) AF: 0.419 AC: 6381 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1606 AN: 5158

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4964 AN: 10536

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37620 AN: 67962

Other (OTH) AF: 0.537 AC: 1127 AN: 2100

Alfa AF: 0.533 Hom.: 26987

Bravo AF: 0.510

Asia WGS AF: 0.449 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		-0.0090
PromoterAI		0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs660975; hg19: chr1-210001048;