rs768275

chr16-60809584-C-G

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 0.111 in 151,552 control chromosomes in the GnomAD database, including 2,096 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 0.11 (2096 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.111 AC: 16787 AN: 151432 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0514

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.111 AC: 16808 AN: 151552 Hom.: 2096 Cov.: 31 AF XY: 0.113 AC XY: 8369 AN XY: 74050

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.0514

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0705 Hom.: 162

Bravo AF: 0.122

Asia WGS AF: 0.150 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.39
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768275; hg19: chr16-60843488;