11-35075448-G-T

Variant names:

• chr11-35075448-G-T
• rs429503
• ENST00000747995.1:n.136+12609G>T

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+12609G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,002 control chromosomes in the GnomAD database, including 37,106 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 0.68 (37106 hom., cov: 31)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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+12609G>T		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-12990G>T		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-12990G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103523 AN: 151884 Hom.: 37048 Cov.: 31

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.682 AC: 103634 AN: 152002 Hom.: 37106 Cov.: 31 AF XY: 0.684 AC XY: 50839 AN XY: 74298

African (AFR) AF: 0.907 AC: 37659 AN: 41532

American (AMR) AF: 0.668 AC: 10206 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4072 AN: 5180

South Asian (SAS) AF: 0.779 AC: 3758 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5655 AN: 10496

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37907 AN: 67912

Other (OTH) AF: 0.684 AC: 1437 AN: 2102

Alfa AF: 0.625 Hom.: 3848

Bravo AF: 0.697

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.28
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs429503; hg19: chr11-35096995;