rs1794899

chr12-121105170-A-Gchr12-121105170-A-T

Variant summary

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

The XR_945458.2(LOC105370031):n.1515-149T>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 0.813 in 152,144 control chromosomes in the GnomAD database, including 51,263 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 0.81 (51263 hom., cov: 32)
• Consequence: LOC105370031 XR_945458.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

Genes affected

LOC105370031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370031	XR_945458.2	n.1515-149T>C		intron_variant, non_coding_transcript_variant
LOC105370031	XR_945457.2	n.2320-149T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123639 AN: 152026 Hom.: 51234 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.813 AC: 123716 AN: 152144 Hom.: 51263 Cov.: 32 AF XY: 0.818 AC XY: 60863 AN XY: 74382

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.829

Alfa AF: 0.863 Hom.: 27536

Bravo AF: 0.803

Asia WGS AF: 0.846 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	13
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1794899; hg19: chr12-121542973;