12-16904489-T-G

Position:

• chr12-16904489-T-G

Variant summary

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

The XR_931397.3(LOC105369677):​n.409-28047A>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 0.58 in 151,932 control chromosomes in the GnomAD database, including 26,195 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 0.58 (26195 hom., cov: 32)
• Consequence: LOC105369677 XR_931397.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87

Genes affected

LOC105369677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369677	XR_931397.3	n.409-28047A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87974 AN: 151814 Hom.: 26170 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.580 AC: 88051 AN: 151932 Hom.: 26195 Cov.: 32 AF XY: 0.581 AC XY: 43104 AN XY: 74228

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.602

Alfa AF: 0.525 Hom.: 40834

Bravo AF: 0.596

Asia WGS AF: 0.627 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs978561; hg19: chr12-17057423;