ENST00000441638.2:n.154+6465A>G

Variant names:

• chr11-131241118-A-G
• rs1793791
• ENST00000441638.2:n.154+6465A>G

Variant summary

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

The ENST00000441638.2(ENSG00000237612):​n.154+6465A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,102 control chromosomes in the GnomAD database, including 10,692 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 0.35 (10692 hom., cov: 33)
• Consequence: ENSG00000237612 ENST00000441638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 2 publications found

Genes affected

ENSG00000237612 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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
ENSG00000237612	ENST00000441638.2	n.154+6465A>G		intron_variant	Intron 1 of 1	4
ENSG00000237612	ENST00000767604.1	n.348-10246A>G		intron_variant	Intron 2 of 2
ENSG00000237612	ENST00000767605.1	n.299-10246A>G		intron_variant	Intron 2 of 2
ENSG00000237612	ENST00000767607.1	n.167-778A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52806 AN: 151984 Hom.: 10679 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.347 AC: 52819 AN: 152102 Hom.: 10692 Cov.: 33 AF XY: 0.350 AC XY: 26015 AN XY: 74350

African (AFR) AF: 0.131 AC: 5441 AN: 41512

American (AMR) AF: 0.340 AC: 5206 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1203 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2465 AN: 5146

South Asian (SAS) AF: 0.340 AC: 1641 AN: 4822

European-Finnish (FIN) AF: 0.493 AC: 5217 AN: 10574

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30329 AN: 67970

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.400 Hom.: 7481

Bravo AF: 0.326

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1793791; hg19: chr11-131111013;