chr8-115318626-G-A

Variant names:

• chr8-115318626-G-A
• rs6983039
• ENST00000748853.1:n.352-39458G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000748853.1(ENSG00000297548):​n.352-39458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 150,486 control chromosomes in the GnomAD database, including 1,141 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 0.10 (1141 hom., cov: 31)
• Consequence: ENSG00000297548 ENST00000748853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 3 publications found

Genes affected

ENSG00000297548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748853.1. 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
	ENSG00000297548	ENST00000748853.1		n.352-39458G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15198 AN: 150438 Hom.: 1149 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0871

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.101 AC: 15208 AN: 150486 Hom.: 1141 Cov.: 31 AF XY: 0.102 AC XY: 7516 AN XY: 73342

African (AFR) AF: 0.211 AC: 8654 AN: 40970

American (AMR) AF: 0.108 AC: 1626 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 218 AN: 3468

East Asian (EAS) AF: 0.0524 AC: 268 AN: 5110

South Asian (SAS) AF: 0.119 AC: 567 AN: 4758

European-Finnish (FIN) AF: 0.0557 AC: 558 AN: 10024

Middle Eastern (MID) AF: 0.0915 AC: 26 AN: 284

European-Non Finnish (NFE) AF: 0.0450 AC: 3046 AN: 67758

Other (OTH) AF: 0.0889 AC: 185 AN: 2080

Alfa AF: 0.113 Hom.: 570

Bravo AF: 0.105

Asia WGS AF: 0.107 AC: 370 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	1.3
DANN	Benign	0.49
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6983039; hg19: chr8-116330855;