rs3892756

chr12-121116865-A-C

Variant summary

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

The XR_007063493.1(LOC105370030):n.181A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152,202 control chromosomes in the GnomAD database, including 470 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 0.066 (470 hom., cov: 32)
• Consequence: LOC105370030 XR_007063493.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

LOC105370030 (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 (NFE) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370030	XR_007063493.1	n.181A>C		non_coding_transcript_exon_variant	2/3
LOC105370030	XR_007063494.1	n.193A>C		non_coding_transcript_exon_variant	2/3
LOC105370030	XR_945453.3	n.193A>C		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10070 AN: 152084 Hom.: 470 Cov.: 32

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0661 AC: 10065 AN: 152202 Hom.: 470 Cov.: 32 AF XY: 0.0659 AC XY: 4906 AN XY: 74414

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0794 Hom.: 156

Bravo AF: 0.0621

Asia WGS AF: 0.0160 AC: 58 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	5.4
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3892756; hg19: chr12-121554668;