rs2507717

chr8-36527313-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656455.1(ENSG00000253363):n.485-100249A>G variant causes a intron, non coding transcript 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: ENST00000656455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656455.1	n.485-100249A>G		intron_variant, non_coding_transcript_variant
	ENST00000651399.1	n.517-31601A>G		intron_variant, non_coding_transcript_variant

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;