8-10558507-A-G

Variant names:

• chr8-10558507-A-G
• rs6601491

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 0.274 in 152,206 control chromosomes in the GnomAD database, including 6,021 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 0.27 (6021 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.275 AC: 41767 AN: 152088 Hom.: 6022 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.274 AC: 41767 AN: 152206 Hom.: 6021 Cov.: 33 AF XY: 0.275 AC XY: 20469 AN XY: 74410

African (AFR) AF: 0.182 AC: 7570 AN: 41542

American (AMR) AF: 0.279 AC: 4274 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1315 AN: 5170

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4820

European-Finnish (FIN) AF: 0.359 AC: 3799 AN: 10586

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20973 AN: 67998

Other (OTH) AF: 0.306 AC: 646 AN: 2114

Alfa AF: 0.303 Hom.: 5185

Bravo AF: 0.271

Asia WGS AF: 0.277 AC: 966 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	2.4
DANN	Benign	0.49
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs6601491; hg19: chr8-10416017;