8-6878491-G-C

Variant names:

• chr8-6878491-G-C
• rs2702876
• ENST00000531701.2:n.602-6631G>C

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.602-6631G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,740 control chromosomes in the GnomAD database, including 7,918 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 0.32 (7918 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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.602-6631G>C		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-6631G>C		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-6631G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48345 AN: 151622 Hom.: 7909 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.319 AC: 48377 AN: 151740 Hom.: 7918 Cov.: 31 AF XY: 0.316 AC XY: 23408 AN XY: 74148

African (AFR) AF: 0.302 AC: 12474 AN: 41356

American (AMR) AF: 0.323 AC: 4928 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2308 AN: 5110

South Asian (SAS) AF: 0.378 AC: 1813 AN: 4792

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10522

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22198 AN: 67926

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.163 Hom.: 313

Bravo AF: 0.326

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2702876; hg19: chr8-6736013;