8-6879513-C-G

Variant names:

• chr8-6879513-C-G
• rs5743407
• ENST00000531701.2:n.602-5609C>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.602-5609C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,578 control chromosomes in the GnomAD database, including 9,796 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 0.35 (9796 hom., cov: 29)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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.602-5609C>G		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-5609C>G		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-5609C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53719 AN: 151462 Hom.: 9788 Cov.: 29

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.355 AC: 53737 AN: 151578 Hom.: 9796 Cov.: 29 AF XY: 0.362 AC XY: 26791 AN XY: 74046

African (AFR) AF: 0.298 AC: 12343 AN: 41380

American (AMR) AF: 0.334 AC: 5101 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.393 AC: 1963 AN: 4994

South Asian (SAS) AF: 0.431 AC: 2060 AN: 4780

European-Finnish (FIN) AF: 0.519 AC: 5476 AN: 10542

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24657 AN: 67854

Other (OTH) AF: 0.334 AC: 700 AN: 2096

Alfa AF: 0.243 Hom.: 662

Bravo AF: 0.336

Asia WGS AF: 0.347 AC: 1209 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	2.9
DANN	Benign	0.60
PhyloP100		0.29

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: rs5743407;

hg19: chr8-6737035;