rs1772810

Positions:

• chr10-117397974-A-C

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 0.271 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.253

Alfa AF: 0.296 Hom.: 9783

Bravo AF: 0.269

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1772810; hg19: chr10-119157485;