rs985729

Variant names:

• chr16-24383130-T-C
• rs985729

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 0.539 in 152,050 control chromosomes in the GnomAD database, including 22,626 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 0.54 (22626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.539 AC: 81825 AN: 151932 Hom.: 22602 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.539 AC: 81900 AN: 152050 Hom.: 22626 Cov.: 32 AF XY: 0.541 AC XY: 40224 AN XY: 74336

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.530

Alfa AF: 0.497 Hom.: 39026

Bravo AF: 0.545

Asia WGS AF: 0.535 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985729; hg19: chr16-24394451;