chr11-100632801-G-A

Variant names:

• chr11-100632801-G-A
• rs11224336
• ENST00000835923.1:n.336-2761C>T

Variant summary

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

The ENST00000835923.1(ENSG00000308712):​n.336-2761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 152,226 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: 0.577
• 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=-0.85).
• 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.336-2761C>T		intron_variant	Intron 1 of 1
ENSG00000308712	ENST00000835924.1	n.269-1193C>T		intron_variant	Intron 1 of 2
ENSG00000308712	ENST00000835925.1	n.254-1193C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11228 AN: 152108 Hom.: 579 Cov.: 33

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0603

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0737 AC: 11226 AN: 152226 Hom.: 577 Cov.: 33 AF XY: 0.0740 AC XY: 5505 AN XY: 74422

African (AFR) AF: 0.0175 AC: 727 AN: 41560

American (AMR) AF: 0.0686 AC: 1050 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1169 AN: 5174

South Asian (SAS) AF: 0.0606 AC: 292 AN: 4820

European-Finnish (FIN) AF: 0.0971 AC: 1028 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0925 AC: 6288 AN: 68002

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0740 Hom.: 63

Bravo AF: 0.0703

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	-0.85
CADD	Benign	3.1
DANN	Benign	0.35
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs11224336; hg19: chr11-100503532;