rs740753

Variant names:

• chr17-61419566-T-C
• rs740753

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 0.15 in 151,902 control chromosomes in the GnomAD database, including 2,445 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 0.15 (2445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 6 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 = 0.287 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22642 AN: 151780 Hom.: 2426 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.150 AC: 22710 AN: 151902 Hom.: 2445 Cov.: 31 AF XY: 0.154 AC XY: 11432 AN XY: 74262

African (AFR) AF: 0.287 AC: 11861 AN: 41384

American (AMR) AF: 0.199 AC: 3047 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1533 AN: 5122

South Asian (SAS) AF: 0.127 AC: 609 AN: 4804

European-Finnish (FIN) AF: 0.111 AC: 1169 AN: 10554

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3989 AN: 67978

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.0896 Hom.: 3952

Bravo AF: 0.164

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.32
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs740753; hg19: chr17-59496927;