17-56604970-A-C

Variant names:

• chr17-56604970-A-C
• rs12603626

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 0.568 in 152,024 control chromosomes in the GnomAD database, including 25,599 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 0.57 (25599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86266 AN: 151906 Hom.: 25586 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.568 AC: 86318 AN: 152024 Hom.: 25599 Cov.: 32 AF XY: 0.574 AC XY: 42670 AN XY: 74288

African (AFR) AF: 0.383 AC: 15873 AN: 41460

American (AMR) AF: 0.628 AC: 9597 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2109 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3918 AN: 5162

South Asian (SAS) AF: 0.748 AC: 3610 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6483 AN: 10558

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42605 AN: 67962

Other (OTH) AF: 0.597 AC: 1258 AN: 2108

Alfa AF: 0.590 Hom.: 3442

Bravo AF: 0.557

Asia WGS AF: 0.743 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs12603626; hg19: chr17-54682331;