rs6474089

Positions:

• chr8-56928101-C-T

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 0.191 in 152,038 control chromosomes in the GnomAD database, including 3,768 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 0.19 (3768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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: 0.191 AC: 28942 AN: 151920 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.191 AC: 28983 AN: 152038 Hom.: 3768 Cov.: 32 AF XY: 0.187 AC XY: 13870 AN XY: 74324

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0978

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.182

Alfa AF: 0.152 Hom.: 381

Bravo AF: 0.200

Asia WGS AF: 0.176 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
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: rs6474089; hg19: chr8-57840660;