rs2527756

Variant names:

• chr8-5545215-T-C
• rs2527756
• ENST00000804953.1:n.335-313T>C

Variant summary

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

The ENST00000804953.1(ENSG00000304614):​n.335-313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,114 control chromosomes in the GnomAD database, including 5,570 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 0.26 (5570 hom., cov: 33)
• Consequence: ENSG00000304614 ENST00000804953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 1 publications found

Genes affected

ENSG00000304614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377793	XR_941372.2	n.222-313T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304614	ENST00000804953.1	n.335-313T>C		intron_variant	Intron 4 of 4
ENSG00000304614	ENST00000804954.1	n.258-313T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38883 AN: 151996 Hom.: 5569 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.256 AC: 38889 AN: 152114 Hom.: 5570 Cov.: 33 AF XY: 0.251 AC XY: 18687 AN XY: 74340

African (AFR) AF: 0.141 AC: 5873 AN: 41518

American (AMR) AF: 0.217 AC: 3313 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3468

East Asian (EAS) AF: 0.188 AC: 972 AN: 5166

South Asian (SAS) AF: 0.347 AC: 1671 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2574 AN: 10570

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

European-Non Finnish (NFE) AF: 0.334 AC: 22720 AN: 67970

Other (OTH) AF: 0.259 AC: 548 AN: 2114

Alfa AF: 0.277 Hom.: 1107

Bravo AF: 0.248

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2527756; hg19: chr8-5402737;