12-105427670-A-G

Position:

• chr12-105427670-A-G

Variant summary

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

The XR_945295.3(LOC105369955):​n.352+697A>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 0.15 in 152,138 control chromosomes in the GnomAD database, including 1,826 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 0.15 (1826 hom., cov: 32)
• Consequence: LOC105369955 XR_945295.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

LOC105369955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369955	XR_945295.3	n.352+697A>G		intron_variant, non_coding_transcript_variant
LOC105369956	XR_945297.3	n.495-907T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22805 AN: 152020 Hom.: 1828 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.150 AC: 22809 AN: 152138 Hom.: 1826 Cov.: 32 AF XY: 0.150 AC XY: 11138 AN XY: 74380

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.161

Alfa AF: 0.159 Hom.: 2396

Bravo AF: 0.150

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11112522; hg19: chr12-105821448;