ENST00000747995.1:n.136+4699T>C

Variant names:

• chr11-35067538-T-C
• rs2732546
• ENST00000747995.1:n.136+4699T>C

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+4699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,920 control chromosomes in the GnomAD database, including 20,153 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 0.50 (20153 hom., cov: 31)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 6 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747995.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297460	ENST00000747995.1		n.136+4699T>C		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.84+17413T>C		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.83+17413T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75272 AN: 151802 Hom.: 20150 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.496 AC: 75279 AN: 151920 Hom.: 20153 Cov.: 31 AF XY: 0.501 AC XY: 37225 AN XY: 74258

African (AFR) AF: 0.279 AC: 11559 AN: 41436

American (AMR) AF: 0.600 AC: 9153 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3899 AN: 5176

South Asian (SAS) AF: 0.689 AC: 3314 AN: 4808

European-Finnish (FIN) AF: 0.522 AC: 5498 AN: 10528

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37890 AN: 67926

Other (OTH) AF: 0.538 AC: 1138 AN: 2116

Alfa AF: 0.391 Hom.: 1224

Bravo AF: 0.490

Asia WGS AF: 0.685 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2732546; hg19: chr11-35089085;