rs740754

Variant names:

• chr17-61419499-T-A
• rs740754

Your query was ambiguous. Multiple possible variants found:

• chr17-61419499-T-A
• chr17-61419499-T-G

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 0.0966 in 151,982 control chromosomes in the GnomAD database, including 978 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 0.097 (978 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.993
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 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: 0.0964 AC: 14640 AN: 151864 Hom.: 969 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.0966 AC: 14679 AN: 151982 Hom.: 978 Cov.: 31 AF XY: 0.102 AC XY: 7594 AN XY: 74294

African (AFR) AF: 0.103 AC: 4262 AN: 41418

American (AMR) AF: 0.179 AC: 2742 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 169 AN: 3464

East Asian (EAS) AF: 0.300 AC: 1544 AN: 5140

South Asian (SAS) AF: 0.126 AC: 608 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1172 AN: 10566

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3934 AN: 67986

Other (OTH) AF: 0.0910 AC: 192 AN: 2110

Alfa AF: 0.0688 Hom.: 65

Bravo AF: 0.102

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs740754; hg19: chr17-59496860;