12-6345932-T-G

Variant names:

• chr12-6345932-T-G
• rs11064145
• XR_002957396.2:n.129T>G

Variant summary

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

The XR_002957396.2(LOC112268088):​n.129T>G 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 0.486 in 152,060 control chromosomes in the GnomAD database, including 18,548 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 0.49 (18548 hom., cov: 32)
• Consequence: LOC112268088 XR_002957396.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 20 publications found

Genes affected

LOC112268088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268088	XR_002957396.2	n.129T>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73884 AN: 151942 Hom.: 18545 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.486 AC: 73922 AN: 152060 Hom.: 18548 Cov.: 32 AF XY: 0.485 AC XY: 36037 AN XY: 74332

African (AFR) AF: 0.601 AC: 24924 AN: 41472

American (AMR) AF: 0.474 AC: 7243 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1185 AN: 5164

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4895 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30606 AN: 67960

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.453 Hom.: 18739

Bravo AF: 0.488

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11064145; hg19: chr12-6455098;