chr1-182571014-T-C

Variant names:

• chr1-182571014-T-C
• rs10911099

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 0.0952 in 152,196 control chromosomes in the GnomAD database, including 836 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 0.095 (836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14498 AN: 152080 Hom.: 839 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0952 AC: 14494 AN: 152196 Hom.: 836 Cov.: 32 AF XY: 0.0951 AC XY: 7077 AN XY: 74428

African (AFR) AF: 0.0439 AC: 1822 AN: 41532

American (AMR) AF: 0.105 AC: 1607 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3464

East Asian (EAS) AF: 0.100 AC: 520 AN: 5184

South Asian (SAS) AF: 0.186 AC: 899 AN: 4826

European-Finnish (FIN) AF: 0.0726 AC: 770 AN: 10600

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7860 AN: 67986

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.113 Hom.: 2317

Bravo AF: 0.0935

Asia WGS AF: 0.164 AC: 569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.82
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs10911099; hg19: chr1-182540149;