12-63157374-T-C

Variant names:

• chr12-63157374-T-C
• rs10877970
• ENST00000789342.1:n.114+1005A>G

Variant summary

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

The ENST00000789342.1(ENSG00000302754):​n.114+1005A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,070 control chromosomes in the GnomAD database, including 8,312 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 0.26 (8312 hom., cov: 32)
• Consequence: ENSG00000302754 ENST00000789342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 5 publications found

Genes affected

ENSG00000302754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789342.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302754	ENST00000789342.1		n.114+1005A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40121 AN: 151952 Hom.: 8286 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0866

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.264 AC: 40191 AN: 152070 Hom.: 8312 Cov.: 32 AF XY: 0.261 AC XY: 19380 AN XY: 74322

African (AFR) AF: 0.575 AC: 23833 AN: 41454

American (AMR) AF: 0.155 AC: 2375 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0866 AC: 300 AN: 3464

East Asian (EAS) AF: 0.149 AC: 770 AN: 5176

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4814

European-Finnish (FIN) AF: 0.140 AC: 1486 AN: 10580

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9372 AN: 67992

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.114 Hom.: 302

Bravo AF: 0.273

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10877970;

hg19: chr12-63551154;