chr17-61415353-A-G

Variant names:

• chr17-61415353-A-G
• rs758598

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 0.609 in 151,966 control chromosomes in the GnomAD database, including 28,914 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 0.61 (28914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.609 AC: 92543 AN: 151848 Hom.: 28889 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.609 AC: 92610 AN: 151966 Hom.: 28914 Cov.: 32 AF XY: 0.616 AC XY: 45737 AN XY: 74292

African (AFR) AF: 0.466 AC: 19296 AN: 41384

American (AMR) AF: 0.617 AC: 9430 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3361 AN: 5164

South Asian (SAS) AF: 0.611 AC: 2941 AN: 4816

European-Finnish (FIN) AF: 0.736 AC: 7777 AN: 10564

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45258 AN: 67974

Other (OTH) AF: 0.618 AC: 1302 AN: 2106

Alfa AF: 0.580 Hom.: 7064

Bravo AF: 0.595

Asia WGS AF: 0.595 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.83
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs758598; hg19: chr17-59492714;