12-119543772-T-C

Variant names:

• chr12-119543772-T-C
• rs708891
• ENST00000509470.2:n.418+9776A>G

Variant summary

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

The ENST00000509470.2(ENSG00000248636):​n.418+9776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,950 control chromosomes in the GnomAD database, including 3,809 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 0.20 (3809 hom., cov: 31)
• Consequence: ENSG00000248636 ENST00000509470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

ENSG00000248636 (HGNC:58183):

LOC105370027 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370027	NR_188489.1	n.885+9776A>G		intron_variant	Intron 2 of 2
LOC105370027	NR_188490.1	n.283+9776A>G		intron_variant	Intron 2 of 3
LOC105370027	NR_188492.1	n.283+9776A>G		intron_variant	Intron 2 of 2
LOC105370027	NR_188494.1	n.283+9776A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248636	ENST00000509470.2	n.418+9776A>G		intron_variant	Intron 2 of 2	1
ENSG00000248636	ENST00000535511.5	n.157+9776A>G		intron_variant	Intron 2 of 2	3
ENSG00000248636	ENST00000537366.5	n.235+9776A>G		intron_variant	Intron 2 of 3	3
ENSG00000248636	ENST00000665601.1	n.159+9776A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30398 AN: 151832 Hom.: 3812 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.200 AC: 30418 AN: 151950 Hom.: 3809 Cov.: 31 AF XY: 0.204 AC XY: 15128 AN XY: 74260

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.208

Alfa AF: 0.149 Hom.: 1154

Bravo AF: 0.212

Asia WGS AF: 0.430 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708891; hg19: chr12-119981577; COSMIC: COSV59543138;