rs2741135

Variant names:

• chr8-6878732-G-A
• rs2741135
• ENST00000531701.2:n.602-6390G>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.602-6390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,916 control chromosomes in the GnomAD database, including 6,884 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 0.29 (6884 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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.602-6390G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-6390G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-6390G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44459 AN: 151798 Hom.: 6880 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.293 AC: 44484 AN: 151916 Hom.: 6884 Cov.: 31 AF XY: 0.290 AC XY: 21507 AN XY: 74242

African (AFR) AF: 0.219 AC: 9086 AN: 41416

American (AMR) AF: 0.308 AC: 4699 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2321 AN: 5144

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4814

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10532

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22157 AN: 67960

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.289 Hom.: 842

Bravo AF: 0.298

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2741135; hg19: chr8-6736254;