chr11-100641161-T-C

Variant names:

• chr11-100641161-T-C
• rs916482
• ENST00000835861.1:n.172+5854T>C

Variant summary

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

The ENST00000835861.1(ENSG00000308695):​n.172+5854T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 138,488 control chromosomes in the GnomAD database, including 12,822 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 0.44 (12822 hom., cov: 31)
• Consequence: ENSG00000308695 ENST00000835861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 3 publications found

Genes affected

ENSG00000308695 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835861.1. 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
	ENSG00000308695	ENST00000835861.1		n.172+5854T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 60695 AN: 138388 Hom.: 12809 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.439 AC: 60742 AN: 138488 Hom.: 12822 Cov.: 31 AF XY: 0.446 AC XY: 30047 AN XY: 67380

African (AFR) AF: 0.364 AC: 12673 AN: 34796

American (AMR) AF: 0.498 AC: 6947 AN: 13944

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1481 AN: 3318

East Asian (EAS) AF: 0.746 AC: 3773 AN: 5058

South Asian (SAS) AF: 0.570 AC: 2408 AN: 4226

European-Finnish (FIN) AF: 0.481 AC: 4734 AN: 9850

Middle Eastern (MID) AF: 0.387 AC: 103 AN: 266

European-Non Finnish (NFE) AF: 0.428 AC: 27476 AN: 64258

Other (OTH) AF: 0.414 AC: 796 AN: 1924

Alfa AF: 0.403 Hom.: 1546

Bravo AF: 0.400

Asia WGS AF: 0.552 AC: 1904 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-0.85

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: rs916482;

hg19: chr11-100511892;