ENST00000747995.1:n.275-11157G>A

Variant names:

• chr11-35107625-G-A
• rs507230
• ENST00000747995.1:n.275-11157G>A

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.275-11157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,100 control chromosomes in the GnomAD database, including 29,770 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 0.61 (29770 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 19 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297460	ENST00000747995.1	n.275-11157G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93181 AN: 151982 Hom.: 29708 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.613 AC: 93304 AN: 152100 Hom.: 29770 Cov.: 32 AF XY: 0.615 AC XY: 45706 AN XY: 74318

African (AFR) AF: 0.757 AC: 31419 AN: 41484

American (AMR) AF: 0.684 AC: 10474 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3785 AN: 5188

South Asian (SAS) AF: 0.772 AC: 3721 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4681 AN: 10550

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35199 AN: 67970

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.545 Hom.: 23173

Bravo AF: 0.634

Asia WGS AF: 0.758 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.16
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs507230; hg19: chr11-35129172;