chr8-6879098-C-A

Variant names:

• chr8-6879098-C-A
• rs5743409
• ENST00000531701.2:n.602-6024C>A

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.602-6024C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 150,954 control chromosomes in the GnomAD database, including 12,763 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 (12763 hom., cov: 28)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-6024C>A		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-6024C>A		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-6024C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61208 AN: 150836 Hom.: 12760 Cov.: 28

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.406 AC: 61218 AN: 150954 Hom.: 12763 Cov.: 28 AF XY: 0.411 AC XY: 30306 AN XY: 73722

African (AFR) AF: 0.308 AC: 12666 AN: 41140

American (AMR) AF: 0.396 AC: 6012 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1338 AN: 3460

East Asian (EAS) AF: 0.392 AC: 1941 AN: 4948

South Asian (SAS) AF: 0.442 AC: 2102 AN: 4756

European-Finnish (FIN) AF: 0.573 AC: 5995 AN: 10468

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29878 AN: 67696

Other (OTH) AF: 0.395 AC: 830 AN: 2102

Alfa AF: 0.421 Hom.: 1686

Bravo AF: 0.386

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.35
DANN	Benign	0.85
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5743409; hg19: chr8-6736620;