17-61419916-A-G

Variant names:

• chr17-61419916-A-G
• rs757608

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 0.707 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.707 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

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.675

Alfa AF: 0.671 Hom.: 78860

Bravo AF: 0.706

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.1
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: rs757608; hg19: chr17-59497277;