ENST00000747995.1:n.136+10246A>G

Variant names:

• chr11-35073085-A-G
• rs1116471
• ENST00000747995.1:n.136+10246A>G

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+10246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,044 control chromosomes in the GnomAD database, including 20,329 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 (20329 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297460	ENST00000747995.1		n.136+10246A>G		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-15353A>G		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-15353A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76398 AN: 151926 Hom.: 20324 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.503 AC: 76415 AN: 152044 Hom.: 20329 Cov.: 32 AF XY: 0.508 AC XY: 37771 AN XY: 74306

African (AFR) AF: 0.324 AC: 13452 AN: 41466

American (AMR) AF: 0.599 AC: 9156 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3903 AN: 5192

South Asian (SAS) AF: 0.688 AC: 3322 AN: 4828

European-Finnish (FIN) AF: 0.514 AC: 5422 AN: 10540

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37215 AN: 67956

Other (OTH) AF: 0.538 AC: 1137 AN: 2112

Alfa AF: 0.521 Hom.: 4366

Bravo AF: 0.498

Asia WGS AF: 0.684 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1116471; hg19: chr11-35094632;