rs6565051

chr16-82625123-G-Achr16-82625123-G-Cchr16-82625123-G-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 0.721 in 152,148 control chromosomes in the GnomAD database, including 39,872 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 0.72 (39872 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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: 0.721 AC: 109625 AN: 152030 Hom.: 39843 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.721 AC: 109694 AN: 152148 Hom.: 39872 Cov.: 33 AF XY: 0.723 AC XY: 53787 AN XY: 74404

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.673

Alfa AF: 0.728 Hom.: 17771

Bravo AF: 0.700

Asia WGS AF: 0.653 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
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: rs6565051; hg19: chr16-82658728;