17-56624581-T-C

Variant names:

• chr17-56624581-T-C
• rs1076352

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 0.864 in 152,256 control chromosomes in the GnomAD database, including 58,183 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 0.86 (58183 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.864 AC: 131417 AN: 152136 Hom.: 58153 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.864 AC: 131497 AN: 152256 Hom.: 58183 Cov.: 33 AF XY: 0.870 AC XY: 64750 AN XY: 74460

African (AFR) AF: 0.648 AC: 26895 AN: 41504

American (AMR) AF: 0.921 AC: 14098 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3155 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5188 AN: 5190

South Asian (SAS) AF: 0.984 AC: 4744 AN: 4822

European-Finnish (FIN) AF: 0.968 AC: 10276 AN: 10616

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64150 AN: 68032

Other (OTH) AF: 0.871 AC: 1844 AN: 2116

Alfa AF: 0.928 Hom.: 41328

Bravo AF: 0.849

Asia WGS AF: 0.968 AC: 3366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.47
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1076352; hg19: chr17-54701942;