rs2182406

Variant names:

• chr10-127768401-A-G
• rs2182406

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 0.692 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.423 AC: 17528 AN: 41450

American (AMR) AF: 0.809 AC: 12350 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2633 AN: 3466

East Asian (EAS) AF: 0.839 AC: 4345 AN: 5176

South Asian (SAS) AF: 0.706 AC: 3402 AN: 4820

European-Finnish (FIN) AF: 0.788 AC: 8335 AN: 10572

Middle Eastern (MID) AF: 0.793 AC: 230 AN: 290

European-Non Finnish (NFE) AF: 0.797 AC: 54200 AN: 67968

Other (OTH) AF: 0.708 AC: 1494 AN: 2110

Alfa AF: 0.770 Hom.: 169215

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2182406; hg19: chr10-129566665;