rs247616

Variant names:

• chr16-56955678-C-T
• rs247616

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 0.291 in 150,764 control chromosomes in the GnomAD database, including 6,577 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 0.29 (6577 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 116 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.291 AC: 43869 AN: 150674 Hom.: 6574 Cov.: 30

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.291 AC: 43893 AN: 150764 Hom.: 6577 Cov.: 30 AF XY: 0.290 AC XY: 21342 AN XY: 73658

African (AFR) AF: 0.256 AC: 10531 AN: 41174

American (AMR) AF: 0.287 AC: 4340 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3464

East Asian (EAS) AF: 0.165 AC: 852 AN: 5152

South Asian (SAS) AF: 0.334 AC: 1603 AN: 4806

European-Finnish (FIN) AF: 0.276 AC: 2752 AN: 9986

Middle Eastern (MID) AF: 0.236 AC: 68 AN: 288

European-Non Finnish (NFE) AF: 0.324 AC: 21921 AN: 67754

Other (OTH) AF: 0.266 AC: 556 AN: 2094

Alfa AF: 0.311 Hom.: 22704

Bravo AF: 0.288

Asia WGS AF: 0.220 AC: 766 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.53
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs247616; hg19: chr16-56989590;