rs6474089

Variant names:

• chr8-56928101-C-T
• rs6474089

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 0.191 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.376 AC: 15579 AN: 41418

American (AMR) AF: 0.123 AC: 1887 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.132 AC: 682 AN: 5170

South Asian (SAS) AF: 0.140 AC: 671 AN: 4808

European-Finnish (FIN) AF: 0.0978 AC: 1036 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8144 AN: 67978

Other (OTH) AF: 0.182 AC: 384 AN: 2114

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6474089; hg19: chr8-57840660;