rs3763894

Variant names:

• chr11-123209897-G-T
• rs3763894
• ENST00000531681.2:n.306-2480G>T

Variant summary

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

The ENST00000531681.2(ENSG00000254710):​n.306-2480G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,180 control chromosomes in the GnomAD database, including 2,149 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 0.12 (2149 hom., cov: 31)
• Consequence: ENSG00000254710 ENST00000531681.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ENSG00000254710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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
ENSG00000254710	ENST00000531681.2	n.306-2480G>T		intron_variant	Intron 3 of 4	3
ENSG00000302758	ENST00000789350.1	n.202+1677C>A		intron_variant	Intron 1 of 1
ENSG00000302758	ENST00000789351.1	n.172-602C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17880 AN: 152062 Hom.: 2146 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.118 AC: 17916 AN: 152180 Hom.: 2149 Cov.: 31 AF XY: 0.116 AC XY: 8607 AN XY: 74416

African (AFR) AF: 0.308 AC: 12752 AN: 41468

American (AMR) AF: 0.0774 AC: 1183 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5180

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4822

European-Finnish (FIN) AF: 0.0613 AC: 651 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2611 AN: 68032

Other (OTH) AF: 0.0979 AC: 206 AN: 2104

Alfa AF: 0.0933 Hom.: 195

Bravo AF: 0.129

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	-0.91
CADD	Benign	0.085
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3763894; hg19: chr11-123080605;