rs10202231

Variant names:

• chr2-60273009-T-A
• rs10202231

Your query was ambiguous. Multiple possible variants found:

• chr2-60273009-T-A
• chr2-60273009-T-G

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 0.485 in 152,142 control chromosomes in the GnomAD database, including 18,134 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 0.48 (18134 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.507 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: 0.485 AC: 73687 AN: 152024 Hom.: 18124 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.485 AC: 73713 AN: 152142 Hom.: 18134 Cov.: 33 AF XY: 0.482 AC XY: 35855 AN XY: 74386

African (AFR) AF: 0.422 AC: 17533 AN: 41520

American (AMR) AF: 0.514 AC: 7856 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1595 AN: 3462

East Asian (EAS) AF: 0.500 AC: 2592 AN: 5186

South Asian (SAS) AF: 0.422 AC: 2032 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5593 AN: 10572

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34764 AN: 67984

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.502 Hom.: 10721

Bravo AF: 0.490

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.059
DANN	Benign	0.52
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10202231; hg19: chr2-60500144;