rs1076392

Variant names:

• chr17-61415647-T-C
• rs1076392

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 0.61 in 152,102 control chromosomes in the GnomAD database, including 28,947 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 (28947 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.610 AC: 92640 AN: 151982 Hom.: 28922 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.610 AC: 92707 AN: 152102 Hom.: 28947 Cov.: 33 AF XY: 0.616 AC XY: 45771 AN XY: 74352

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.616

Alfa AF: 0.628 Hom.: 5272

Bravo AF: 0.595

Asia WGS AF: 0.594 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1076392; hg19: chr17-59493008;