8-142683195-G-T

Variant names:

• chr8-142683195-G-T
• rs2976397

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 0.37 in 152,084 control chromosomes in the GnomAD database, including 11,375 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 0.37 (11375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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: 0.370 AC: 56201 AN: 151964 Hom.: 11360 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.370 AC: 56239 AN: 152084 Hom.: 11375 Cov.: 32 AF XY: 0.372 AC XY: 27624 AN XY: 74328

African (AFR) AF: 0.201 AC: 8338 AN: 41524

American (AMR) AF: 0.478 AC: 7309 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1218 AN: 5152

South Asian (SAS) AF: 0.360 AC: 1733 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5164 AN: 10574

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29425 AN: 67948

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.395 Hom.: 22052

Bravo AF: 0.361

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2976397; hg19: chr8-143764613;