chr8-142040310-T-C

Variant names:

• chr8-142040310-T-C
• rs4917300

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 0.565 in 152,056 control chromosomes in the GnomAD database, including 24,517 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 0.56 (24517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85808 AN: 151938 Hom.: 24496 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.565 AC: 85877 AN: 152056 Hom.: 24517 Cov.: 32 AF XY: 0.563 AC XY: 41832 AN XY: 74330

African (AFR) AF: 0.634 AC: 26272 AN: 41462

American (AMR) AF: 0.607 AC: 9274 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3572 AN: 5158

South Asian (SAS) AF: 0.530 AC: 2552 AN: 4816

European-Finnish (FIN) AF: 0.447 AC: 4724 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.530 AC: 36000 AN: 67984

Other (OTH) AF: 0.556 AC: 1176 AN: 2114

Alfa AF: 0.541 Hom.: 101849

Bravo AF: 0.579

Asia WGS AF: 0.582 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4917300; hg19: chr8-143121671;