chr17-61617277-T-C

Position:

• chr17-61617277-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.3 in 152,122 control chromosomes in the GnomAD database, including 7,073 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 0.30 (7073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45655 AN: 152004 Hom.: 7062 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.300 AC: 45699 AN: 152122 Hom.: 7073 Cov.: 32 AF XY: 0.298 AC XY: 22200 AN XY: 74382

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.311

Alfa AF: 0.292 Hom.: 1353

Bravo AF: 0.307

Asia WGS AF: 0.330 AC: 1145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	22
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040609; hg19: chr17-59694638;