2-135728401-T-C

Variant names:

• chr2-135728401-T-C
• rs724326
• ENST00000836082.1:n.93+13214A>G

Variant summary

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

The ENST00000836082.1(ENSG00000308733):​n.93+13214A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,032 control chromosomes in the GnomAD database, including 9,233 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 0.31 (9233 hom., cov: 32)
• Consequence: ENSG00000308733 ENST00000836082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 9 publications found

Genes affected

ENSG00000308733 (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 = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836082.1. 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
	ENSG00000308733	ENST00000836082.1		n.93+13214A>G		intron	N/A
	ENSG00000308733	ENST00000836083.1		n.81+13214A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46422 AN: 151914 Hom.: 9212 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.306 AC: 46509 AN: 152032 Hom.: 9233 Cov.: 32 AF XY: 0.306 AC XY: 22736 AN XY: 74308

African (AFR) AF: 0.518 AC: 21472 AN: 41468

American (AMR) AF: 0.319 AC: 4862 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3466

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5166

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1625 AN: 10570

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11879 AN: 67958

Other (OTH) AF: 0.348 AC: 735 AN: 2112

Alfa AF: 0.229 Hom.: 5131

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.53
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs724326; hg19: chr2-136485971;