chr12-91932724-T-C

Position:

• chr12-91932724-T-C

Variant summary

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

The XR_007063580.1(LOC105369901):​n.842-3373A>G 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 0.568 in 151,806 control chromosomes in the GnomAD database, including 25,705 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 0.57 (25705 hom., cov: 32)
• Consequence: LOC105369901 XR_007063580.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

LOC105369901 (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	Protein	UniProt
LOC105369901	XR_007063580.1	n.842-3373A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86243 AN: 151688 Hom.: 25698 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.568 AC: 86280 AN: 151806 Hom.: 25705 Cov.: 32 AF XY: 0.571 AC XY: 42393 AN XY: 74216

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.611

Alfa AF: 0.613 Hom.: 15064

Bravo AF: 0.561

Asia WGS AF: 0.675 AC: 2342 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11106345; hg19: chr12-92326500;