chr8-29613431-T-C

Position:

• chr8-29613431-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.492 in 152,134 control chromosomes in the GnomAD database, including 19,508 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 0.49 (19508 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74710 AN: 152014 Hom.: 19471 Cov.: 34

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.492 AC: 74800 AN: 152134 Hom.: 19508 Cov.: 34 AF XY: 0.482 AC XY: 35837 AN XY: 74374

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.490

Alfa AF: 0.462 Hom.: 2127

Bravo AF: 0.508

Asia WGS AF: 0.309 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6558132; hg19: chr8-29470947;