chr10-2062221-G-A

Position:

• chr10-2062221-G-A

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 0.621 in 151,972 control chromosomes in the GnomAD database, including 29,776 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 0.62 (29776 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94236 AN: 151854 Hom.: 29713 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.621 AC: 94366 AN: 151972 Hom.: 29776 Cov.: 31 AF XY: 0.614 AC XY: 45611 AN XY: 74268

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.598

Alfa AF: 0.578 Hom.: 50225

Bravo AF: 0.634

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388121; hg19: chr10-2104415;