11-35071523-A-G

Variant names:

• chr11-35071523-A-G
• rs2785197
• ENST00000747995.1:n.136+8684A>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+8684A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,056 control chromosomes in the GnomAD database, including 20,495 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 0.51 (20495 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 21 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297460	ENST00000747995.1		n.136+8684A>G		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-16915A>G		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-16915A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76919 AN: 151938 Hom.: 20489 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.506 AC: 76942 AN: 152056 Hom.: 20495 Cov.: 32 AF XY: 0.512 AC XY: 38040 AN XY: 74338

African (AFR) AF: 0.336 AC: 13950 AN: 41468

American (AMR) AF: 0.600 AC: 9175 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3904 AN: 5186

South Asian (SAS) AF: 0.689 AC: 3323 AN: 4826

European-Finnish (FIN) AF: 0.514 AC: 5415 AN: 10534

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37228 AN: 67974

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.523 Hom.: 22459

Bravo AF: 0.502

Asia WGS AF: 0.686 AC: 2381 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2785197;

hg19: chr11-35093070;