chr8-6878545-G-C

Variant names:

• chr8-6878545-G-C
• rs2702877
• ENST00000531701.2:n.602-6577G>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.602-6577G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,968 control chromosomes in the GnomAD database, including 39,599 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 0.72 (39599 hom., cov: 32)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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.602-6577G>C		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-6577G>C		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-6577G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109431 AN: 151850 Hom.: 39589 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.721 AC: 109493 AN: 151968 Hom.: 39599 Cov.: 32 AF XY: 0.724 AC XY: 53761 AN XY: 74262

African (AFR) AF: 0.670 AC: 27757 AN: 41424

American (AMR) AF: 0.710 AC: 10851 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3470

East Asian (EAS) AF: 0.852 AC: 4393 AN: 5154

South Asian (SAS) AF: 0.804 AC: 3867 AN: 4812

European-Finnish (FIN) AF: 0.737 AC: 7770 AN: 10540

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49775 AN: 67984

Other (OTH) AF: 0.742 AC: 1562 AN: 2106

Alfa AF: 0.721 Hom.: 4910

Bravo AF: 0.713

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2702877; hg19: chr8-6736067;