11-100632623-C-T

Variant names:

• chr11-100632623-C-T
• rs11224335
• ENST00000835923.1:n.336-2583G>A

Variant summary

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

The ENST00000835923.1(ENSG00000308712):​n.336-2583G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 152,256 control chromosomes in the GnomAD database, including 577 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 0.074 (577 hom., cov: 33)
• Consequence: ENSG00000308712 ENST00000835923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 1 publications found

Genes affected

ENSG00000308712 (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 = 0.215 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
ENSG00000308712	ENST00000835923.1	n.336-2583G>A		intron_variant	Intron 1 of 1
ENSG00000308712	ENST00000835924.1	n.269-1015G>A		intron_variant	Intron 1 of 2
ENSG00000308712	ENST00000835925.1	n.254-1015G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11237 AN: 152138 Hom.: 579 Cov.: 33

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.0974

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.0738 AC: 11235 AN: 152256 Hom.: 577 Cov.: 33 AF XY: 0.0740 AC XY: 5508 AN XY: 74448

African (AFR) AF: 0.0174 AC: 725 AN: 41552

American (AMR) AF: 0.0687 AC: 1051 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5174

South Asian (SAS) AF: 0.0601 AC: 290 AN: 4826

European-Finnish (FIN) AF: 0.0974 AC: 1032 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0926 AC: 6297 AN: 68024

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0767 Hom.: 66

Bravo AF: 0.0704

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11224335; hg19: chr11-100503354;