8-6879674-A-G

Variant names:

• chr8-6879674-A-G
• rs2741136
• ENST00000531701.2:n.602-5448A>G

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.602-5448A>G variant causes a intron 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 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-5448A>G		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-5448A>G		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-5448A>G		intron	N/A

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

African (AFR) AF: 0.321 AC: 13292 AN: 41418

American (AMR) AF: 0.336 AC: 5135 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.148 AC: 762 AN: 5134

South Asian (SAS) AF: 0.189 AC: 913 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3040 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21121 AN: 67976

Other (OTH) AF: 0.297 AC: 627 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.15
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2741136; hg19: chr8-6737196;