8-119527903-C-T

Variant names:

• chr8-119527903-C-T
• rs9643136

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.419 in 151,942 control chromosomes in the GnomAD database, including 14,234 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 0.42 (14234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 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: 0.419 AC: 63668 AN: 151822 Hom.: 14231 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.419 AC: 63692 AN: 151942 Hom.: 14234 Cov.: 31 AF XY: 0.425 AC XY: 31559 AN XY: 74242

African (AFR) AF: 0.268 AC: 11101 AN: 41426

American (AMR) AF: 0.498 AC: 7605 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2036 AN: 5166

South Asian (SAS) AF: 0.589 AC: 2835 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5502 AN: 10544

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31524 AN: 67934

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.458 Hom.: 9961

Bravo AF: 0.406

Asia WGS AF: 0.515 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.27
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9643136; hg19: chr8-120540143;