rs740754

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.993

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.61419499T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0910

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740754; hg19: chr17-59496860;