rs13171512

Variant names:

• chr5-68669204-C-T
• rs13171512
• ENST00000507733.3:n.314-51689G>A

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.314-51689G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,078 control chromosomes in the GnomAD database, including 38,411 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 0.69 (38411 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 6 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=-0.85).
• 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.441-51689G>A		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.111-51689G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.314-51689G>A		intron_variant	Intron 2 of 5	2
ENSG00000248884	ENST00000688207.1	n.66-51689G>A		intron_variant	Intron 1 of 2
ENSG00000248884	ENST00000717704.1	n.111-51689G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105489 AN: 151960 Hom.: 38410 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.694 AC: 105516 AN: 152078 Hom.: 38411 Cov.: 32 AF XY: 0.690 AC XY: 51315 AN XY: 74332

African (AFR) AF: 0.518 AC: 21490 AN: 41448

American (AMR) AF: 0.574 AC: 8779 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1849 AN: 5158

South Asian (SAS) AF: 0.706 AC: 3399 AN: 4816

European-Finnish (FIN) AF: 0.836 AC: 8844 AN: 10582

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.823 AC: 55981 AN: 68000

Other (OTH) AF: 0.711 AC: 1503 AN: 2114

Alfa AF: 0.787 Hom.: 24389

Bravo AF: 0.662

Asia WGS AF: 0.548 AC: 1908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.64
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13171512; hg19: chr5-67965031;