rs10202231

Positions:

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

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 0.485 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.509

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10202231; hg19: chr2-60500144;