rs1772810

Variant names:

• chr10-117397974-A-C
• rs1772810

Your query was ambiguous. Multiple possible variants found:

• chr10-117397974-A-C
• chr10-117397974-A-G
• chr10-117397974-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 0.271 in 152,076 control chromosomes in the GnomAD database, including 5,935 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 0.27 (5935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.271 AC: 41145 AN: 151958 Hom.: 5934 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.271 AC: 41149 AN: 152076 Hom.: 5935 Cov.: 32 AF XY: 0.260 AC XY: 19356 AN XY: 74350

African (AFR) AF: 0.257 AC: 10659 AN: 41470

American (AMR) AF: 0.203 AC: 3094 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3472

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5182

South Asian (SAS) AF: 0.303 AC: 1456 AN: 4800

European-Finnish (FIN) AF: 0.196 AC: 2073 AN: 10590

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21490 AN: 67968

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.293 Hom.: 22118

Bravo AF: 0.269

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs1772810; hg19: chr10-119157485;