ENST00000507733.3:n.313+20071G>T

Variant names:

• chr5-68725382-C-A
• rs27545
• ENST00000507733.3:n.313+20071G>T

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.313+20071G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,956 control chromosomes in the GnomAD database, including 9,971 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 0.36 (9971 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 1 publications found

Genes affected

ENSG00000248884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.440+103326G>T		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.110+34206G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.313+20071G>T		intron_variant	Intron 2 of 5	2
ENSG00000248884	ENST00000688207.1	n.65+34206G>T		intron_variant	Intron 1 of 2
ENSG00000248884	ENST00000717704.1	n.110+34206G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54078 AN: 151838 Hom.: 9972 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.356 AC: 54093 AN: 151956 Hom.: 9971 Cov.: 32 AF XY: 0.352 AC XY: 26156 AN XY: 74234

African (AFR) AF: 0.410 AC: 16979 AN: 41414

American (AMR) AF: 0.260 AC: 3978 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3468

East Asian (EAS) AF: 0.115 AC: 596 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1911 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3555 AN: 10524

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24719 AN: 67970

Other (OTH) AF: 0.371 AC: 782 AN: 2108

Alfa AF: 0.343 Hom.: 12414

Bravo AF: 0.346

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs27545; hg19: chr5-68021209; COSMIC: COSV60152098;