rs10801629

Variant names:

• chr1-197875237-C-T
• rs10801629

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 0.422 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.422 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

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.416

Alfa AF: 0.412 Hom.: 26460

Bravo AF: 0.423

Asia WGS AF: 0.423 AC: 1469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10801629; hg19: chr1-197844367;