11-35075211-T-C

Variant names:

• chr11-35075211-T-C
• rs2553826
• ENST00000747995.1:n.136+12372T>C

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+12372T>C 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 152,012 control chromosomes in the GnomAD database, including 21,567 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 (21567 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• 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=-0.9).
• 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

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+12372T>C		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.85-13227T>C		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.84-13227T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79802 AN: 151894 Hom.: 21561 Cov.: 32

Gnomad AFR AF: 0.403

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: 0.514

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.525 AC: 79829 AN: 152012 Hom.: 21567 Cov.: 32 AF XY: 0.530 AC XY: 39370 AN XY: 74284

African (AFR) AF: 0.403 AC: 16707 AN: 41448

American (AMR) AF: 0.607 AC: 9266 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2115 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3883 AN: 5192

South Asian (SAS) AF: 0.689 AC: 3325 AN: 4824

European-Finnish (FIN) AF: 0.514 AC: 5413 AN: 10532

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

European-Non Finnish (NFE) AF: 0.548 AC: 37242 AN: 67960

Other (OTH) AF: 0.560 AC: 1184 AN: 2114

Alfa AF: 0.523 Hom.: 2546

Bravo AF: 0.524

Asia WGS AF: 0.686 AC: 2379 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.76
PhyloP100		-0.99

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: rs2553826;

hg19: chr11-35096758;