rs7398018

chr12-131554797-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063534.1(LOC124903056):n.176+3258G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,168 control chromosomes in the GnomAD database, including 12,907 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 0.39 (12907 hom., cov: 33)
• Consequence: LOC124903056 XR_007063534.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

LOC124903056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903056	XR_007063534.1	n.176+3258G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58987 AN: 152050 Hom.: 12890 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.388 AC: 59031 AN: 152168 Hom.: 12907 Cov.: 33 AF XY: 0.384 AC XY: 28551 AN XY: 74378

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.431

Alfa AF: 0.427 Hom.: 2458

Bravo AF: 0.385

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7398018; hg19: chr12-132039342;