rs2507717

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000253363 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253363	ENST00000651399.1	n.517-31601A>G		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.1	n.485-100249A>G		intron_variant	Intron 4 of 5

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.179

Alfa AF: 0.122 Hom.: 707

Bravo AF: 0.186

Asia WGS AF: 0.278 AC: 962 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2507717; hg19: chr8-36384831;