rs11226613

Variant names:

• chr11-105101791-T-A
• rs11226613
• ENST00000798071.1:n.221-4296T>A

Variant summary

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

The ENST00000798071.1(ENSG00000303918):​n.221-4296T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,048 control chromosomes in the GnomAD database, including 2,812 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 0.18 (2812 hom., cov: 32)
• Consequence: ENSG00000303918 ENST00000798071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 6 publications found

Genes affected

ENSG00000303918 (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 (EAS) allele frequency at 95% confidence interval = 0.323 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
ENSG00000303918	ENST00000798071.1	n.221-4296T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27102 AN: 151932 Hom.: 2817 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.178 AC: 27089 AN: 152048 Hom.: 2812 Cov.: 32 AF XY: 0.179 AC XY: 13333 AN XY: 74308

African (AFR) AF: 0.0807 AC: 3351 AN: 41512

American (AMR) AF: 0.202 AC: 3083 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3462

East Asian (EAS) AF: 0.336 AC: 1731 AN: 5152

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1793 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14221 AN: 67968

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.189 Hom.: 376

Bravo AF: 0.175

Asia WGS AF: 0.236 AC: 822 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	0.39
DANN	Benign	0.74
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11226613; hg19: chr11-104972518;