chr12-131455375-G-T

Variant names:

• chr12-131455375-G-T
• rs10466868
• NR_187798.1:n.3486C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187798.1(LOC101929974):​n.3486C>A 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 0.0741 in 152,576 control chromosomes in the GnomAD database, including 576 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 0.074 (575 hom., cov: 33)
  • Exomes 𝑓: 0.090 (1 hom.)
• Consequence: LOC101929974 NR_187798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 12 publications found

Genes affected

LOC101929974 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929974	NR_187798.1	n.3486C>A		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256209	ENST00000618927.1	n.39+23C>A		intron_variant	Intron 1 of 4	4
ENSG00000256209	ENST00000833770.1	n.1092-40C>A		intron_variant	Intron 3 of 4
ENSG00000256209	ENST00000833771.1	n.703-40C>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11285 AN: 152058 Hom.: 575 Cov.: 33

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0791

GnomAD4 exome AF: 0.0900 AC: 36 AN: 400 Hom.: 1 Cov.: 0 AF XY: 0.100 AC XY: 30 AN XY: 300

African (AFR) AF: 0.00 AC: 0 AN: 10

American (AMR) AF: 0.00 AC: 0 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.100 AC: 2 AN: 20

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0920 AC: 30 AN: 326

Other (OTH) AF: 0.0833 AC: 2 AN: 24

GnomAD4 genome AF: 0.0741 AC: 11275 AN: 152176 Hom.: 575 Cov.: 33 AF XY: 0.0723 AC XY: 5378 AN XY: 74396

African (AFR) AF: 0.0194 AC: 806 AN: 41522

American (AMR) AF: 0.0848 AC: 1295 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4824

European-Finnish (FIN) AF: 0.0704 AC: 746 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7249 AN: 67994

Other (OTH) AF: 0.0778 AC: 164 AN: 2108

Alfa AF: 0.0947 Hom.: 2367

Bravo AF: 0.0723

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	4.8
DANN	Benign	0.62
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10466868; hg19: chr12-131939920;