chr1-111287011-C-A

Variant names:

• chr1-111287011-C-A
• rs10857871

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 0.816 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
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.813 AC: 33716 AN: 41484

American (AMR) AF: 0.866 AC: 13220 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5101 AN: 5144

South Asian (SAS) AF: 0.839 AC: 4046 AN: 4822

European-Finnish (FIN) AF: 0.796 AC: 8402 AN: 10552

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.796 AC: 54085 AN: 67986

Other (OTH) AF: 0.812 AC: 1713 AN: 2110

Alfa AF: 0.806 Hom.: 30663

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10857871; hg19: chr1-111829633;