ENST00000748002.1:n.441G>A

Variant names:

• chr11-35088128-G-A
• rs1365057
• ENST00000748002.1:n.441G>A

Variant summary

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

The ENST00000748002.1(ENSG00000297460):​n.441G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,150 control chromosomes in the GnomAD database, including 4,636 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 0.24 (4636 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000748002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748002.1. 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
	ENSG00000297460	ENST00000748002.1		n.441G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000297460	ENST00000748003.1		n.107G>A		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000297460	ENST00000747995.1		n.137-310G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36873 AN: 152032 Hom.: 4648 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36871 AN: 152150 Hom.: 4636 Cov.: 32 AF XY: 0.242 AC XY: 17996 AN XY: 74392

African (AFR) AF: 0.229 AC: 9515 AN: 41504

American (AMR) AF: 0.285 AC: 4354 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2034 AN: 5186

South Asian (SAS) AF: 0.155 AC: 747 AN: 4822

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15618 AN: 67990

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.234 Hom.: 18079

Bravo AF: 0.246

Asia WGS AF: 0.292 AC: 1014 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	1.7
DANN	Benign	0.59
PhyloP100		-0.89

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: rs1365057;

hg19: chr11-35109675;