rs3024685

Positions:

• chr16-27365589-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;