17-61419916-A-G

Variant names:

• chr17-61419916-A-G
• rs757608

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 0.707 in 151,966 control chromosomes in the GnomAD database, including 38,282 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 0.71 (38282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107283 AN: 151848 Hom.: 38232 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.707 AC: 107395 AN: 151966 Hom.: 38282 Cov.: 31 AF XY: 0.709 AC XY: 52638 AN XY: 74246

African (AFR) AF: 0.794 AC: 32915 AN: 41456

American (AMR) AF: 0.661 AC: 10093 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2441 AN: 3466

East Asian (EAS) AF: 0.694 AC: 3575 AN: 5148

South Asian (SAS) AF: 0.624 AC: 3004 AN: 4812

European-Finnish (FIN) AF: 0.736 AC: 7761 AN: 10552

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45366 AN: 67944

Other (OTH) AF: 0.675 AC: 1421 AN: 2104

Alfa AF: 0.676 Hom.: 158493

Bravo AF: 0.706

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.1
DANN	Benign	0.74
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs757608; hg19: chr17-59497277;