rs12958098

Positions:

• chr18-22565416-T-C
• chr18-22565416-T-G

Variant summary

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

The XR_007066310.1(LOC124904265):​n.196-17622T>C 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 0.383 in 152,084 control chromosomes in the GnomAD database, including 13,625 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 0.38 (13625 hom., cov: 32)
• Consequence: LOC124904265 XR_007066310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

Genes affected

LOC124904265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904265	XR_007066310.1	n.196-17622T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58269 AN: 151966 Hom.: 13627 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.383 AC: 58266 AN: 152084 Hom.: 13625 Cov.: 32 AF XY: 0.384 AC XY: 28557 AN XY: 74318

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.401

Alfa AF: 0.345 Hom.: 1231

Bravo AF: 0.351

Asia WGS AF: 0.357 AC: 1240 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12958098; hg19: chr18-20145379;