5-68667788-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:58096):

LOC105379013 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507733.3. 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
	ENSG00000248884	ENST00000507733.3	TSL:2	n.314-50273G>A		intron	N/A
	ENSG00000248884	ENST00000688207.1		n.66-50273G>A		intron	N/A
	ENSG00000248884	ENST00000717704.1		n.111-50273G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs7713001;

hg19: chr5-67963615;