rs2336434

Variant names:

• chr12-65125486-T-G
• rs2336434
• ENST00000844184.1:n.164-2436A>C

Variant summary

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

The ENST00000844184.1(ENSG00000289319):​n.164-2436A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0309 in 152,184 control chromosomes in the GnomAD database, including 157 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 0.031 (157 hom., cov: 32)
• Consequence: ENSG00000289319 ENST00000844184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 5 publications found

Genes affected

ENSG00000289319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844184.1. 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
	ENSG00000289319	ENST00000844184.1		n.164-2436A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4694 AN: 152066 Hom.: 155 Cov.: 32

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.000849

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00932

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0309 AC: 4702 AN: 152184 Hom.: 157 Cov.: 32 AF XY: 0.0313 AC XY: 2332 AN XY: 74400

African (AFR) AF: 0.0822 AC: 3411 AN: 41496

American (AMR) AF: 0.0172 AC: 262 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4820

European-Finnish (FIN) AF: 0.000849 AC: 9 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00932 AC: 634 AN: 68026

Other (OTH) AF: 0.0298 AC: 63 AN: 2114

Alfa AF: 0.0204 Hom.: 39

Bravo AF: 0.0328

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.71
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2336434; hg19: chr12-65519266;