rs442432

Variant names:

• chr6-169074813-G-A
• rs442432

Your query was ambiguous. Multiple possible variants found:

• chr6-169074813-G-A
• chr6-169074813-G-C
• chr6-169074813-G-T

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 0.771 in 152,112 control chromosomes in the GnomAD database, including 45,873 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 0.77 (45873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.771 AC: 117193 AN: 151994 Hom.: 45837 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.771 AC: 117277 AN: 152112 Hom.: 45873 Cov.: 32 AF XY: 0.766 AC XY: 56917 AN XY: 74338

African (AFR) AF: 0.902 AC: 37455 AN: 41536

American (AMR) AF: 0.703 AC: 10726 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2475 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3197 AN: 5144

South Asian (SAS) AF: 0.761 AC: 3667 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7069 AN: 10566

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50236 AN: 67998

Other (OTH) AF: 0.745 AC: 1575 AN: 2114

Alfa AF: 0.748 Hom.: 131524

Bravo AF: 0.776

Asia WGS AF: 0.697 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.69
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs442432; hg19: chr6-169474908; COSMIC: COSV69434552;