chr8-41251129-T-C

Variant names:

• chr8-41251129-T-C
• rs7823929

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 0.505 in 152,014 control chromosomes in the GnomAD database, including 20,368 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 0.51 (20368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76725 AN: 151896 Hom.: 20354 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.505 AC: 76800 AN: 152014 Hom.: 20368 Cov.: 32 AF XY: 0.504 AC XY: 37480 AN XY: 74292

African (AFR) AF: 0.677 AC: 28052 AN: 41456

American (AMR) AF: 0.488 AC: 7458 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1918 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2135 AN: 5170

South Asian (SAS) AF: 0.523 AC: 2521 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4701 AN: 10540

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28514 AN: 67966

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.450 Hom.: 59828

Bravo AF: 0.511

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7823929; hg19: chr8-41108648;