chr11-131241118-A-G

Position:

• chr11-131241118-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441638.1(ENSG00000237612):​n.116+6465A>G variant causes a intron, non coding transcript 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: ENST00000441638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000441638.1	n.116+6465A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.360

Alfa AF: 0.400 Hom.: 6753

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1793791; hg19: chr11-131111013;