chr12-127656538-C-G

Variant names:

• chr12-127656538-C-G
• rs1388149
• ENST00000747044.1:n.231-18047C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000747044.1(ENSG00000297305):​n.231-18047C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,812 control chromosomes in the GnomAD database, including 6,777 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 0.29 (6777 hom., cov: 32)
• Consequence: ENSG00000297305 ENST00000747044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 2 publications found

Genes affected

ENSG00000297305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297305	ENST00000747044.1	n.231-18047C>G		intron_variant	Intron 2 of 2
ENSG00000297329	ENST00000747112.1	n.248-5198G>C		intron_variant	Intron 1 of 2
ENSG00000297329	ENST00000747113.1	n.228-5198G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44496 AN: 151698 Hom.: 6765 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.293 AC: 44542 AN: 151812 Hom.: 6777 Cov.: 32 AF XY: 0.296 AC XY: 21953 AN XY: 74160

African (AFR) AF: 0.265 AC: 10973 AN: 41394

American (AMR) AF: 0.371 AC: 5659 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3464

East Asian (EAS) AF: 0.378 AC: 1944 AN: 5142

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2328 AN: 10508

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19477 AN: 67918

Other (OTH) AF: 0.314 AC: 662 AN: 2106

Alfa AF: 0.169 Hom.: 309

Bravo AF: 0.302

Asia WGS AF: 0.367 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.46
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1388149; hg19: chr12-128141083;