chr8-29478491-T-C

Variant names:

• chr8-29478491-T-C
• rs11987193

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 0.709 in 152,134 control chromosomes in the GnomAD database, including 38,641 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 0.71 (38641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 7 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 (SAS) allele frequency at 95% confidence interval = 0.824 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: 0.709 AC: 107853 AN: 152016 Hom.: 38620 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.709 AC: 107924 AN: 152134 Hom.: 38641 Cov.: 32 AF XY: 0.716 AC XY: 53266 AN XY: 74392

African (AFR) AF: 0.605 AC: 25075 AN: 41468

American (AMR) AF: 0.769 AC: 11745 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2486 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3982 AN: 5170

South Asian (SAS) AF: 0.846 AC: 4074 AN: 4818

European-Finnish (FIN) AF: 0.770 AC: 8157 AN: 10600

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50104 AN: 68010

Other (OTH) AF: 0.701 AC: 1483 AN: 2116

Alfa AF: 0.732 Hom.: 173729

Bravo AF: 0.704

Asia WGS AF: 0.819 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.020
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11987193; hg19: chr8-29336008;