11-35074763-A-G

Variant names:

• chr11-35074763-A-G
• rs2098878
• ENST00000747995.1:n.136+11924A>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+11924A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,936 control chromosomes in the GnomAD database, including 21,561 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 0.53 (21561 hom., cov: 31)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 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 = 0.728 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+11924A>G		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-13675A>G		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-13675A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79770 AN: 151818 Hom.: 21555 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.525 AC: 79797 AN: 151936 Hom.: 21561 Cov.: 31 AF XY: 0.530 AC XY: 39367 AN XY: 74280

African (AFR) AF: 0.403 AC: 16689 AN: 41394

American (AMR) AF: 0.607 AC: 9271 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3466

East Asian (EAS) AF: 0.748 AC: 3869 AN: 5172

South Asian (SAS) AF: 0.688 AC: 3313 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37227 AN: 67942

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.411 Hom.: 1178

Bravo AF: 0.524

Asia WGS AF: 0.688 AC: 2392 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	0.34
DANN	Benign	0.75
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2098878; hg19: chr11-35096310;