rs419132

Variant names:

• chr6-32243022-A-G
• rs419132

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 0.375 in 151,974 control chromosomes in the GnomAD database, including 12,262 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 0.38 (12262 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 36 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 (SAS) allele frequency at 95% confidence interval = 0.543 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: 0.375 AC: 56947 AN: 151856 Hom.: 12254 Cov.: 30

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.375 AC: 57009 AN: 151974 Hom.: 12262 Cov.: 30 AF XY: 0.375 AC XY: 27882 AN XY: 74310

African (AFR) AF: 0.524 AC: 21676 AN: 41380

American (AMR) AF: 0.401 AC: 6126 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2296 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2518 AN: 5150

South Asian (SAS) AF: 0.561 AC: 2699 AN: 4814

European-Finnish (FIN) AF: 0.157 AC: 1665 AN: 10596

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18700 AN: 67986

Other (OTH) AF: 0.441 AC: 929 AN: 2108

Alfa AF: 0.339 Hom.: 13802

Bravo AF: 0.398

Asia WGS AF: 0.499 AC: 1734 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	1.3
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs419132; hg19: chr6-32210799;