8-6879713-A-G

Variant names:

• chr8-6879713-A-G
• rs2741137
• ENST00000531701.1:n.226-5409A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531701.1(GS1-24F4.2):​n.226-5409A>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 ENST00000531701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000531701.1	n.226-5409A>G		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.713

Alfa AF: 0.707 Hom.: 6333

Bravo AF: 0.757

Asia WGS AF: 0.637 AC: 2216 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	1.0
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741137; hg19: chr8-6737235;