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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804953.1. 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
	ENSG00000304614	ENST00000804953.1		n.335-313T>C		intron	N/A
	ENSG00000304614	ENST00000804954.1		n.258-313T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2527756;

hg19: chr8-5402737;