rs13233731

Variant names:

• chr7-130752930-G-A
• rs13233731
• XR_007060527.1:n.178+14940G>A

Variant summary

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

The XR_007060527.1(LOC105375508):​n.178+14940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,912 control chromosomes in the GnomAD database, including 13,006 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 0.40 (13006 hom., cov: 31)
• Consequence: LOC105375508 XR_007060527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 40 publications found

Genes affected

LOC105375508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375508	XR_007060527.1	n.178+14940G>A		intron_variant	Intron 3 of 4
LOC105375508	XR_927976.3	n.178+14940G>A		intron_variant	Intron 3 of 5
LOC105375508	XR_927977.3	n.178+14940G>A		intron_variant	Intron 3 of 3
LOC105375508	XR_927978.3	n.178+14940G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61018 AN: 151794 Hom.: 13002 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.402 AC: 61035 AN: 151912 Hom.: 13006 Cov.: 31 AF XY: 0.398 AC XY: 29573 AN XY: 74246

African (AFR) AF: 0.272 AC: 11277 AN: 41430

American (AMR) AF: 0.388 AC: 5917 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1587 AN: 5164

South Asian (SAS) AF: 0.386 AC: 1851 AN: 4800

European-Finnish (FIN) AF: 0.449 AC: 4736 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33103 AN: 67922

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.438 Hom.: 2651

Bravo AF: 0.391

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.42
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs13233731; hg19: chr7-130437689;