rs993226

chr12-84492794-T-G

Variant summary

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

The XR_945151.2(LOC105369875):n.333A>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 0.0612 in 152,140 control chromosomes in the GnomAD database, including 432 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 0.061 (432 hom., cov: 32)
• Consequence: LOC105369875 XR_945151.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878

Genes affected

LOC105369875 (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 (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369875	XR_945151.2	n.333A>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9297 AN: 152022 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0161

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0612 AC: 9307 AN: 152140 Hom.: 432 Cov.: 32 AF XY: 0.0575 AC XY: 4276 AN XY: 74376

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0355

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.0159

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0418 Hom.: 114

Bravo AF: 0.0660

Asia WGS AF: 0.0160 AC: 56 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	7.5
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs993226; hg19: chr12-84886573;