chr12-64403625-T-C

Variant names:

• chr12-64403625-T-C
• rs7397470
• ENST00000718893.1:n.173-328A>G

Variant summary

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

The ENST00000718893.1(ENSG00000293771):​n.173-328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,260 control chromosomes in the GnomAD database, including 3,587 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 0.19 (3587 hom., cov: 33)
• Consequence: ENSG00000293771 ENST00000718893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 5 publications found

Genes affected

ENSG00000293771 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718893.1. 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
	ENSG00000293771	ENST00000718893.1		n.173-328A>G		intron	N/A
	ENSG00000293771	ENST00000718894.1		n.179+457A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29419 AN: 152142 Hom.: 3589 Cov.: 33

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.193 AC: 29412 AN: 152260 Hom.: 3587 Cov.: 33 AF XY: 0.196 AC XY: 14556 AN XY: 74454

African (AFR) AF: 0.0484 AC: 2014 AN: 41588

American (AMR) AF: 0.221 AC: 3376 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1267 AN: 5176

South Asian (SAS) AF: 0.197 AC: 952 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2901 AN: 10586

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17722 AN: 68014

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.232 Hom.: 12992

Bravo AF: 0.183

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.72
PhyloP100		-0.058

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: rs7397470;

hg19: chr12-64797405;