8-119495498-T-C

Variant names:

• chr8-119495498-T-C
• rs7000665

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 0.498 in 151,698 control chromosomes in the GnomAD database, including 19,053 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 0.50 (19053 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 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: 0.498 AC: 75416 AN: 151580 Hom.: 19019 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.498 AC: 75508 AN: 151698 Hom.: 19053 Cov.: 31 AF XY: 0.503 AC XY: 37264 AN XY: 74118

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.486

Alfa AF: 0.477 Hom.: 8870

Bravo AF: 0.499

Asia WGS AF: 0.589 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7000665; hg19: chr8-120507738;