rs10801629

Positions:

• chr1-197875237-C-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 0.422 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;