11-33895919-A-T

Variant names:

• chr11-33895919-A-T
• rs750781
• ENST00000834606.1:n.90+1884A>T

Variant summary

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

The ENST00000834606.1(ENSG00000308500):​n.90+1884A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,066 control chromosomes in the GnomAD database, including 34,750 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 0.65 (34750 hom., cov: 32)
• Consequence: ENSG00000308500 ENST00000834606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 1 publications found

Genes affected

ENSG00000308500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376621	XR_931176.3	n.90+1884A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308500	ENST00000834606.1	n.90+1884A>T		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834607.1	n.135+1884A>T		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834608.1	n.91+1884A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98500 AN: 151950 Hom.: 34757 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.648 AC: 98502 AN: 152066 Hom.: 34750 Cov.: 32 AF XY: 0.650 AC XY: 48290 AN XY: 74346

African (AFR) AF: 0.357 AC: 14782 AN: 41442

American (AMR) AF: 0.622 AC: 9504 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2441 AN: 3464

East Asian (EAS) AF: 0.607 AC: 3136 AN: 5164

South Asian (SAS) AF: 0.716 AC: 3453 AN: 4822

European-Finnish (FIN) AF: 0.845 AC: 8968 AN: 10610

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53812 AN: 67970

Other (OTH) AF: 0.652 AC: 1376 AN: 2112

Alfa AF: 0.712 Hom.: 5008

Bravo AF: 0.619

Asia WGS AF: 0.588 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs750781; hg19: chr11-33917466;