ENST00000507733.3:n.347-52252A>T

Variant names:

• chr5-68486729-T-A
• rs56103849
• ENST00000507733.3:n.347-52252A>T

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.347-52252A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,844 control chromosomes in the GnomAD database, including 27,506 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 0.60 (27506 hom., cov: 31)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.474-53144A>T		intron_variant	Intron 3 of 4
LOC105379013	XR_007058805.1	n.144-53144A>T		intron_variant	Intron 2 of 3
LOC105379013	XR_007058806.1	n.2260-53144A>T		intron_variant	Intron 2 of 3
LOC105379012	XR_948411.3	n.302+2991T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.347-52252A>T		intron_variant	Intron 3 of 5	2
ENSG00000248884	ENST00000701911.2	n.204+35770A>T		intron_variant	Intron 1 of 1
ENSG00000248884	ENST00000717704.1	n.144-29581A>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90452 AN: 151726 Hom.: 27484 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.596 AC: 90504 AN: 151844 Hom.: 27506 Cov.: 31 AF XY: 0.593 AC XY: 44001 AN XY: 74222

African (AFR) AF: 0.617 AC: 25553 AN: 41384

American (AMR) AF: 0.505 AC: 7695 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2095 AN: 3466

East Asian (EAS) AF: 0.230 AC: 1186 AN: 5160

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4814

European-Finnish (FIN) AF: 0.666 AC: 7016 AN: 10542

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42156 AN: 67920

Other (OTH) AF: 0.570 AC: 1200 AN: 2106

Alfa AF: 0.610 Hom.: 3508

Bravo AF: 0.582

Asia WGS AF: 0.419 AC: 1462 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	3.9
DANN	Benign	0.68
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs56103849; hg19: chr5-67782556; COSMIC: COSV60151346;