rs7017115

Variant names:

• chr8-81511528-A-G
• rs7017115
• ENST00000524085.2:n.435-10179A>G

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.435-10179A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,080 control chromosomes in the GnomAD database, including 9,463 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 0.34 (9463 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524085.2. 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
	ENSG00000253374	ENST00000524085.2	TSL:5	n.435-10179A>G		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.327-10179A>G		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.309-10179A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51988 AN: 151962 Hom.: 9425 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.342 AC: 52082 AN: 152080 Hom.: 9463 Cov.: 32 AF XY: 0.342 AC XY: 25413 AN XY: 74352

African (AFR) AF: 0.447 AC: 18546 AN: 41460

American (AMR) AF: 0.382 AC: 5843 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3472

East Asian (EAS) AF: 0.129 AC: 666 AN: 5180

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2981 AN: 10578

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20216 AN: 67968

Other (OTH) AF: 0.347 AC: 734 AN: 2114

Alfa AF: 0.328 Hom.: 1043

Bravo AF: 0.352

Asia WGS AF: 0.289 AC: 1003 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7017115; hg19: chr8-82423763;