8-128281872-T-C

Variant names:

• chr8-128281872-T-C
• rs1989051

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 0.685 in 151,944 control chromosomes in the GnomAD database, including 36,825 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 0.68 (36825 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.872 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: 0.685 AC: 103970 AN: 151826 Hom.: 36776 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.685 AC: 104081 AN: 151944 Hom.: 36825 Cov.: 31 AF XY: 0.684 AC XY: 50759 AN XY: 74258

African (AFR) AF: 0.880 AC: 36500 AN: 41476

American (AMR) AF: 0.599 AC: 9125 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2237 AN: 3462

East Asian (EAS) AF: 0.666 AC: 3441 AN: 5164

South Asian (SAS) AF: 0.706 AC: 3402 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6192 AN: 10556

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40916 AN: 67912

Other (OTH) AF: 0.674 AC: 1420 AN: 2108

Alfa AF: 0.645 Hom.: 4029

Bravo AF: 0.697

Asia WGS AF: 0.714 AC: 2484 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.85
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1989051; hg19: chr8-129294118;