12-4367051-T-C

Variant names:

• chr12-4367051-T-C
• rs7961824
• ENST00000674624.1:n.*1204+769T>C

Variant summary

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

The ENST00000674624.1(ENSG00000285901):​n.*1204+769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,184 control chromosomes in the GnomAD database, including 4,419 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 0.23 (4419 hom., cov: 32)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 8 publications found

Genes affected

ENSG00000285901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285901	ENST00000674624.1		n.*1204+769T>C		intron	N/A	ENSP00000501898.1
	ENSG00000285901	ENST00000648100.1		n.*1967+769T>C		intron	N/A	ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34824 AN: 152066 Hom.: 4417 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.229 AC: 34824 AN: 152184 Hom.: 4419 Cov.: 32 AF XY: 0.231 AC XY: 17178 AN XY: 74394

African (AFR) AF: 0.113 AC: 4710 AN: 41550

American (AMR) AF: 0.287 AC: 4392 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5176

South Asian (SAS) AF: 0.174 AC: 841 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3517 AN: 10572

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

European-Non Finnish (NFE) AF: 0.273 AC: 18556 AN: 67994

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.261 Hom.: 4383

Bravo AF: 0.220

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.39
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs7961824; hg19: chr12-4476217;