chr8-46012589-G-A

Variant names:

• chr8-46012589-G-A
• rs2353200

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 0.165 in 151,790 control chromosomes in the GnomAD database, including 3,943 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 0.17 (3943 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.165 AC: 24989 AN: 151670 Hom.: 3929 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.165 AC: 25052 AN: 151790 Hom.: 3943 Cov.: 33 AF XY: 0.165 AC XY: 12215 AN XY: 74172

African (AFR) AF: 0.403 AC: 16655 AN: 41352

American (AMR) AF: 0.186 AC: 2845 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3468

East Asian (EAS) AF: 0.128 AC: 647 AN: 5070

South Asian (SAS) AF: 0.128 AC: 618 AN: 4820

European-Finnish (FIN) AF: 0.0648 AC: 685 AN: 10570

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0439 AC: 2979 AN: 67928

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.121 Hom.: 601

Bravo AF: 0.186

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.60

Splicing

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

Other links and lift over

dbSNP: rs2353200; hg19: chr8-46924211;