rs16962449

Variant names:

• chr13-103456264-G-C
• rs16962449

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.376 in 152,016 control chromosomes in the GnomAD database, including 11,660 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 0.38 (11660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.375 AC: 57023 AN: 151900 Hom.: 11634 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.376 AC: 57104 AN: 152016 Hom.: 11660 Cov.: 32 AF XY: 0.374 AC XY: 27799 AN XY: 74288

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.359

Alfa AF: 0.348 Hom.: 1218

Bravo AF: 0.392

Asia WGS AF: 0.330 AC: 1144 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16962449; hg19: chr13-104108614;