rs2741136

Positions:

• chr8-6879674-A-G
• chr8-6879674-A-T

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-5448A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,970 control chromosomes in the GnomAD database, including 7,158 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 0.30 (7158 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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 (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-5448A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46204 AN: 151852 Hom.: 7156 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.304 AC: 46237 AN: 151970 Hom.: 7158 Cov.: 31 AF XY: 0.300 AC XY: 22268 AN XY: 74268

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.297

Alfa AF: 0.314 Hom.: 1168

Bravo AF: 0.313

Asia WGS AF: 0.221 AC: 768 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	0.25
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741136; hg19: chr8-6737196;