rs3024685

Variant names:

• chr16-27365589-T-C
• rs3024685

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 0.51 in 151,636 control chromosomes in the GnomAD database, including 21,625 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 0.51 (21625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.510 AC: 77214 AN: 151518 Hom.: 21577 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.510 AC: 77327 AN: 151636 Hom.: 21625 Cov.: 32 AF XY: 0.508 AC XY: 37685 AN XY: 74138

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.465

Alfa AF: 0.480 Hom.: 1798

Bravo AF: 0.524

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024685; hg19: chr16-27376910;