rs6499500

chr16-71314512-C-Gchr16-71314512-C-T

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 0.654 in 152,058 control chromosomes in the GnomAD database, including 34,169 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 0.65 (34169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.653 AC: 99263 AN: 151940 Hom.: 34109 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.654 AC: 99388 AN: 152058 Hom.: 34169 Cov.: 32 AF XY: 0.650 AC XY: 48313 AN XY: 74312

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.634

Alfa AF: 0.480 Hom.: 1359

Bravo AF: 0.681

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.74
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6499500; hg19: chr16-71348415;