rs11226616

Variant names:

• chr11-97437516-A-C
• rs11226616
• ENST00000742846.1:n.220+5962T>G

Variant summary

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

The ENST00000742846.1(ENSG00000296835):​n.220+5962T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,144 control chromosomes in the GnomAD database, including 340 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 0.062 (340 hom., cov: 32)
• Consequence: ENSG00000296835 ENST00000742846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 5 publications found

Genes affected

ENSG00000296835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296835	ENST00000742846.1	n.220+5962T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9427 AN: 152026 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0621 AC: 9452 AN: 152144 Hom.: 340 Cov.: 32 AF XY: 0.0635 AC XY: 4725 AN XY: 74380

African (AFR) AF: 0.0709 AC: 2945 AN: 41522

American (AMR) AF: 0.0865 AC: 1320 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4826

European-Finnish (FIN) AF: 0.0954 AC: 1011 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0542 AC: 3681 AN: 67976

Other (OTH) AF: 0.0549 AC: 116 AN: 2112

Alfa AF: 0.0600 Hom.: 34

Bravo AF: 0.0619

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.25
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs11226616; hg19: chr11-97308516;