rs4367565

Variant names:

• chr8-130525709-A-G
• rs4367565

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 0.4 in 152,080 control chromosomes in the GnomAD database, including 16,634 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 0.40 (16634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.400 AC: 60766 AN: 151962 Hom.: 16596 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.400 AC: 60858 AN: 152080 Hom.: 16634 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74324

African (AFR) AF: 0.781 AC: 32393 AN: 41470

American (AMR) AF: 0.250 AC: 3828 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 710 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1835 AN: 5158

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4818

European-Finnish (FIN) AF: 0.230 AC: 2433 AN: 10580

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.251 AC: 17082 AN: 67976

Other (OTH) AF: 0.358 AC: 756 AN: 2114

Alfa AF: 0.304 Hom.: 23946

Bravo AF: 0.417

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4367565; hg19: chr8-131537955;