rs2741134

Variant names:

• chr8-6878588-G-A
• rs2741134
• ENST00000531701.2:n.602-6534G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531701.2(GS1-24F4.2):​n.602-6534G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,848 control chromosomes in the GnomAD database, including 8,434 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 0.33 (8434 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 3 publications found

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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
GS1-24F4.2	ENST00000531701.2	n.602-6534G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-6534G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-6534G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50001 AN: 151730 Hom.: 8421 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.330 AC: 50052 AN: 151848 Hom.: 8434 Cov.: 31 AF XY: 0.326 AC XY: 24226 AN XY: 74236

African (AFR) AF: 0.339 AC: 14011 AN: 41378

American (AMR) AF: 0.327 AC: 4987 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2327 AN: 5146

South Asian (SAS) AF: 0.378 AC: 1819 AN: 4806

European-Finnish (FIN) AF: 0.192 AC: 2021 AN: 10532

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22236 AN: 67938

Other (OTH) AF: 0.363 AC: 763 AN: 2102

Alfa AF: 0.324 Hom.: 1942

Bravo AF: 0.339

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.30
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2741134; hg19: chr8-6736110;