rs2310991

Variant names:

• chr10-70171890-C-A
• rs2310991

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 0.44 in 152,014 control chromosomes in the GnomAD database, including 15,374 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 0.44 (15374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.440 AC: 66765 AN: 151896 Hom.: 15342 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.440 AC: 66820 AN: 152014 Hom.: 15374 Cov.: 33 AF XY: 0.440 AC XY: 32688 AN XY: 74310

African (AFR) AF: 0.543 AC: 22517 AN: 41434

American (AMR) AF: 0.334 AC: 5111 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3466

East Asian (EAS) AF: 0.148 AC: 766 AN: 5162

South Asian (SAS) AF: 0.350 AC: 1690 AN: 4826

European-Finnish (FIN) AF: 0.496 AC: 5248 AN: 10572

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.423 AC: 28747 AN: 67956

Other (OTH) AF: 0.419 AC: 887 AN: 2116

Alfa AF: 0.250 Hom.: 579

Bravo AF: 0.428

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2310991; hg19: chr10-71931646;