chr16-24383130-T-C

Variant names:

• chr16-24383130-T-C
• rs985729

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 0.539 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.660 AC: 27344 AN: 41460

American (AMR) AF: 0.510 AC: 7782 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2008 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2181 AN: 5170

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5326 AN: 10580

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32426 AN: 67964

Other (OTH) AF: 0.530 AC: 1120 AN: 2114

Alfa AF: 0.501 Hom.: 81866

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs985729; hg19: chr16-24394451;