rs2738169

Positions:

• chr8-6885036-G-A

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-86G>A 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 0.206 in 152,158 control chromosomes in the GnomAD database, including 3,493 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 0.21 (3493 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-86G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31374 AN: 152018 Hom.: 3486 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.200 AC: 4 AN: 20 Hom.: 0 AF XY: 0.167 AC XY: 3 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.206 AC: 31389 AN: 152138 Hom.: 3493 Cov.: 32 AF XY: 0.214 AC XY: 15896 AN XY: 74372

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.179

Alfa AF: 0.181 Hom.: 5372

Bravo AF: 0.198

Asia WGS AF: 0.262 AC: 909 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	4.5
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738169; hg19: chr8-6742558;