8-9938679-T-C

Position:

• chr8-9938679-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 0.812 in 152,184 control chromosomes in the GnomAD database, including 50,303 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 0.81 (50303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.812 AC: 123532 AN: 152066 Hom.: 50270 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.812 AC: 123617 AN: 152184 Hom.: 50303 Cov.: 32 AF XY: 0.810 AC XY: 60249 AN XY: 74410

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.835

Alfa AF: 0.816 Hom.: 96991

Bravo AF: 0.816

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs615171; hg19: chr8-9796189;