ENST00000531701.2:n.602-5409A>G

Variant names:

• chr8-6879713-A-G
• rs2741137
• ENST00000531701.2:n.602-5409A>G

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.602-5409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,110 control chromosomes in the GnomAD database, including 44,539 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 0.76 (44539 hom., cov: 32)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-5409A>G		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-5409A>G		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-5409A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115257 AN: 151990 Hom.: 44488 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.758 AC: 115363 AN: 152110 Hom.: 44539 Cov.: 32 AF XY: 0.760 AC XY: 56541 AN XY: 74352

African (AFR) AF: 0.901 AC: 37401 AN: 41498

American (AMR) AF: 0.718 AC: 10982 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2415 AN: 3472

East Asian (EAS) AF: 0.547 AC: 2823 AN: 5160

South Asian (SAS) AF: 0.744 AC: 3582 AN: 4812

European-Finnish (FIN) AF: 0.811 AC: 8572 AN: 10570

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47284 AN: 67988

Other (OTH) AF: 0.713 AC: 1507 AN: 2114

Alfa AF: 0.716 Hom.: 12173

Bravo AF: 0.757

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.20
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2741137; hg19: chr8-6737235;