11-35071482-G-A

Variant names:

• chr11-35071482-G-A
• rs2785198
• ENST00000747995.1:n.136+8643G>A

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+8643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,128 control chromosomes in the GnomAD database, including 34,646 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 0.66 (34646 hom., cov: 33)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.832 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+8643G>A		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-16956G>A		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-16956G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100794 AN: 152010 Hom.: 34600 Cov.: 33

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.663 AC: 100893 AN: 152128 Hom.: 34646 Cov.: 33 AF XY: 0.667 AC XY: 49573 AN XY: 74358

African (AFR) AF: 0.839 AC: 34867 AN: 41538

American (AMR) AF: 0.665 AC: 10175 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4100 AN: 5190

South Asian (SAS) AF: 0.781 AC: 3769 AN: 4824

European-Finnish (FIN) AF: 0.540 AC: 5687 AN: 10526

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37933 AN: 67970

Other (OTH) AF: 0.674 AC: 1424 AN: 2112

Alfa AF: 0.614 Hom.: 3668

Bravo AF: 0.677

Asia WGS AF: 0.773 AC: 2688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2785198; hg19: chr11-35093029;