rs660975

chr1-209827703-A-Cchr1-209827703-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.537

Alfa AF: 0.537 Hom.: 20622

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs660975; hg19: chr1-210001048;