rs1424032

Variant names:

• chr16-62933249-A-G
• rs1424032

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 0.16 in 151,806 control chromosomes in the GnomAD database, including 2,191 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 0.16 (2191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 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: 0.160 AC: 24331 AN: 151688 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.160 AC: 24348 AN: 151806 Hom.: 2191 Cov.: 32 AF XY: 0.162 AC XY: 12048 AN XY: 74182

Gnomad4 AFR AF: 0.0817

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.165

Alfa AF: 0.189 Hom.: 4664

Bravo AF: 0.162

Asia WGS AF: 0.154 AC: 538 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	14
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424032; hg19: chr16-62967153;