rs768275

Variant names:

• chr16-60809584-C-G
• rs768275

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.303 AC: 12520 AN: 41356

American (AMR) AF: 0.0801 AC: 1215 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.0514 AC: 178 AN: 3460

East Asian (EAS) AF: 0.177 AC: 902 AN: 5092

South Asian (SAS) AF: 0.140 AC: 676 AN: 4812

European-Finnish (FIN) AF: 0.0253 AC: 269 AN: 10624

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0131 AC: 885 AN: 67732

Other (OTH) AF: 0.0723 AC: 152 AN: 2102

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs768275; hg19: chr16-60843488;