8-17424902-T-C

Position:

• chr8-17424902-T-C

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 0.722 in 152,112 control chromosomes in the GnomAD database, including 41,798 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 0.72 (41798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 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: 0.722 AC: 109761 AN: 151994 Hom.: 41805 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.722 AC: 109781 AN: 152112 Hom.: 41798 Cov.: 32 AF XY: 0.721 AC XY: 53623 AN XY: 74360

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.728

Alfa AF: 0.818 Hom.: 68533

Bravo AF: 0.705

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
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: rs13271465; hg19: chr8-17282411;