chr12-40372127-A-G

Position:

• chr12-40372127-A-G

Variant summary

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

The XR_944868.3(LOC105369736):​n.485-17300T>C 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 0.862 in 151,992 control chromosomes in the GnomAD database, including 56,494 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 0.86 (56494 hom., cov: 32)
• Consequence: LOC105369736 XR_944868.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

LOC105369736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369736	XR_944868.3	n.485-17300T>C		intron_variant, non_coding_transcript_variant
LOC105369736	XR_944869.3	n.485-75T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130881 AN: 151874 Hom.: 56450 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.862 AC: 130981 AN: 151992 Hom.: 56494 Cov.: 32 AF XY: 0.863 AC XY: 64095 AN XY: 74276

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.872

Alfa AF: 0.871 Hom.: 9025

Bravo AF: 0.857

Asia WGS AF: 0.761 AC: 2647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7962370; hg19: chr12-40765929;