rs2182406

Positions:

• chr10-127768401-A-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 0.692 in 152,032 control chromosomes in the GnomAD database, including 38,668 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 0.69 (38668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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: 0.693 AC: 105218 AN: 151914 Hom.: 38646 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.798

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.692 AC: 105275 AN: 152032 Hom.: 38668 Cov.: 32 AF XY: 0.694 AC XY: 51593 AN XY: 74324

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.708

Alfa AF: 0.782 Hom.: 77415

Bravo AF: 0.687

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2182406; hg19: chr10-129566665;