rs4512347

Positions:

• chr8-103392164-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 0.0775 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.0803

Gnomad4 AMR AF: 0.0516

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.0589

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0601 Hom.: 641

Bravo AF: 0.0682

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4512347; hg19: chr8-104404392;