rs2738182

Variant names:

• chr8-6878247-A-T
• rs2738182
• ENST00000531701.2:n.602-6875A>T

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.602-6875A>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 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-6875A>T		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-6875A>T		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-6875A>T		intron	N/A

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

African (AFR) AF: 0.581 AC: 24083 AN: 41466

American (AMR) AF: 0.367 AC: 5606 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2504 AN: 5148

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4808

European-Finnish (FIN) AF: 0.203 AC: 2148 AN: 10602

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23527 AN: 67970

Other (OTH) AF: 0.434 AC: 916 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.49
PhyloP100		-3.1
PromoterAI		0.014	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2738182;

hg19: chr8-6735769;