chr17-45325639-T-C

Variant names:

• chr17-45325639-T-C
• rs4792814

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 0.655 in 152,116 control chromosomes in the GnomAD database, including 33,654 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 0.65 (33654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 25 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 (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.654 AC: 99461 AN: 151998 Hom.: 33604 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.655 AC: 99561 AN: 152116 Hom.: 33654 Cov.: 32 AF XY: 0.654 AC XY: 48617 AN XY: 74372

African (AFR) AF: 0.829 AC: 34394 AN: 41508

American (AMR) AF: 0.511 AC: 7812 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2166 AN: 5176

South Asian (SAS) AF: 0.641 AC: 3093 AN: 4828

European-Finnish (FIN) AF: 0.665 AC: 7036 AN: 10576

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41184 AN: 67958

Other (OTH) AF: 0.630 AC: 1328 AN: 2108

Alfa AF: 0.609 Hom.: 30145

Bravo AF: 0.654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.36
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4792814; hg19: chr17-43403005;