rs10800149

Variant names:

• chr1-165715830-A-C
• rs10800149

Your query was ambiguous. Multiple possible variants found:

• chr1-165715830-A-C
• chr1-165715830-A-T

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 0.559 in 151,918 control chromosomes in the GnomAD database, including 25,203 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 0.56 (25203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84921 AN: 151800 Hom.: 25186 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.559 AC: 84984 AN: 151918 Hom.: 25203 Cov.: 32 AF XY: 0.560 AC XY: 41602 AN XY: 74276

African (AFR) AF: 0.753 AC: 31163 AN: 41406

American (AMR) AF: 0.542 AC: 8277 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4200 AN: 5156

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4816

European-Finnish (FIN) AF: 0.480 AC: 5070 AN: 10552

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30352 AN: 67938

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.488 Hom.: 24389

Bravo AF: 0.575

Asia WGS AF: 0.650 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10800149; hg19: chr1-165685067;