chr8-103392164-T-C

Variant names:

• chr8-103392164-T-C
• rs4512347

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 0.0775 in 152,214 control chromosomes in the GnomAD database, including 570 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 0.077 (570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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: 0.0774 AC: 11776 AN: 152096 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0775 AC: 11794 AN: 152214 Hom.: 570 Cov.: 32 AF XY: 0.0835 AC XY: 6212 AN XY: 74424

African (AFR) AF: 0.0803 AC: 3335 AN: 41536

American (AMR) AF: 0.0516 AC: 789 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.188 AC: 974 AN: 5174

South Asian (SAS) AF: 0.0694 AC: 335 AN: 4826

European-Finnish (FIN) AF: 0.184 AC: 1949 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0589 AC: 4007 AN: 68014

Other (OTH) AF: 0.0626 AC: 132 AN: 2108

Alfa AF: 0.0618 Hom.: 1382

Bravo AF: 0.0682

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.44
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4512347; hg19: chr8-104404392;