rs2507717

Variant names:

• chr8-36527313-T-C
• rs2507717
• ENST00000651399.1:n.517-31601A>G

Variant summary

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

The ENST00000651399.1(ENSG00000253363):​n.517-31601A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,926 control chromosomes in the GnomAD database, including 3,306 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 0.18 (3306 hom., cov: 32)
• Consequence: ENSG00000253363 ENST00000651399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

ENSG00000253363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651399.1. 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
	ENSG00000253363	ENST00000651399.1		n.517-31601A>G		intron	N/A
	ENSG00000253363	ENST00000656455.2		n.485-100249A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27049 AN: 151808 Hom.: 3293 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.178 AC: 27109 AN: 151926 Hom.: 3306 Cov.: 32 AF XY: 0.180 AC XY: 13355 AN XY: 74262

African (AFR) AF: 0.339 AC: 14048 AN: 41408

American (AMR) AF: 0.133 AC: 2027 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1442 AN: 5132

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4828

European-Finnish (FIN) AF: 0.101 AC: 1071 AN: 10592

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6614 AN: 67934

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.122 Hom.: 796

Bravo AF: 0.186

Asia WGS AF: 0.278 AC: 962 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.50
PhyloP100		0.064

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: rs2507717;

hg19: chr8-36384831;