chr5-68667788-C-T

Variant names:

• chr5-68667788-C-T
• rs7713001
• ENST00000507733.3:n.314-50273G>A

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.314-50273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,028 control chromosomes in the GnomAD database, including 38,657 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 0.70 (38657 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.441-50273G>A		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.111-50273G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.314-50273G>A		intron_variant	Intron 2 of 5	2
ENSG00000248884	ENST00000688207.1	n.66-50273G>A		intron_variant	Intron 1 of 2
ENSG00000248884	ENST00000717704.1	n.111-50273G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105867 AN: 151910 Hom.: 38655 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.697 AC: 105897 AN: 152028 Hom.: 38657 Cov.: 32 AF XY: 0.693 AC XY: 51512 AN XY: 74316

African (AFR) AF: 0.527 AC: 21823 AN: 41418

American (AMR) AF: 0.575 AC: 8786 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2649 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1851 AN: 5148

South Asian (SAS) AF: 0.710 AC: 3418 AN: 4812

European-Finnish (FIN) AF: 0.836 AC: 8854 AN: 10596

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55988 AN: 67990

Other (OTH) AF: 0.715 AC: 1511 AN: 2114

Alfa AF: 0.747 Hom.: 71790

Bravo AF: 0.665

Asia WGS AF: 0.549 AC: 1910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.39
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7713001; hg19: chr5-67963615;