rs16962449

chr13-103456264-G-C

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/exons	MANE	UniProt

Ensembl

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