rs2738182

Variant names:

• chr8-6878247-A-T
• rs2738182
• ENST00000531701.1:n.226-6875A>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.226-6875A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,056 control chromosomes in the GnomAD database, including 14,010 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 0.41 (14010 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 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.226-6875A>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62585 AN: 151938 Hom.: 13966 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.412 AC: 62680 AN: 152056 Hom.: 14010 Cov.: 31 AF XY: 0.407 AC XY: 30221 AN XY: 74336

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.434

Alfa AF: 0.373 Hom.: 1400

Bravo AF: 0.432

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738182; hg19: chr8-6735769;