17-6249814-G-A

Position:

• chr17-6249814-G-A

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 0.397 in 152,058 control chromosomes in the GnomAD database, including 12,531 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 0.40 (12531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60306 AN: 151938 Hom.: 12531 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.397 AC: 60328 AN: 152058 Hom.: 12531 Cov.: 32 AF XY: 0.398 AC XY: 29560 AN XY: 74308

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.409

Alfa AF: 0.412 Hom.: 26969

Bravo AF: 0.393

Asia WGS AF: 0.571 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3888640; hg19: chr17-6153134;