1-197875237-C-T

Variant names:

• chr1-197875237-C-T
• rs10801629

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 0.422 in 151,986 control chromosomes in the GnomAD database, including 13,689 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 0.42 (13689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64152 AN: 151868 Hom.: 13672 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.422 AC: 64192 AN: 151986 Hom.: 13689 Cov.: 32 AF XY: 0.418 AC XY: 31051 AN XY: 74286

African (AFR) AF: 0.483 AC: 19986 AN: 41408

American (AMR) AF: 0.368 AC: 5614 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1586 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1749 AN: 5172

South Asian (SAS) AF: 0.458 AC: 2202 AN: 4812

European-Finnish (FIN) AF: 0.370 AC: 3900 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27615 AN: 67992

Other (OTH) AF: 0.416 AC: 877 AN: 2106

Alfa AF: 0.412 Hom.: 53401

Bravo AF: 0.423

Asia WGS AF: 0.423 AC: 1469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.38
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10801629; hg19: chr1-197844367;