rs10857871

Positions:

• chr1-111287011-C-A
• chr1-111287011-C-G
• chr1-111287011-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 0.816 in 152,046 control chromosomes in the GnomAD database, including 50,783 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 0.82 (50783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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: 0.816 AC: 124020 AN: 151928 Hom.: 50747 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.816 AC: 124113 AN: 152046 Hom.: 50783 Cov.: 31 AF XY: 0.819 AC XY: 60821 AN XY: 74290

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.812

Alfa AF: 0.806 Hom.: 28141

Bravo AF: 0.824

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857871; hg19: chr1-111829633;