11-5540365-C-T

Position:

• chr11-5540365-C-T

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+50460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,168 control chromosomes in the GnomAD database, including 67,919 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 0.94 (67919 hom., cov: 30)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5540365C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+50460G>A		intron_variant		5		ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143295 AN: 152050 Hom.: 67882 Cov.: 30

Gnomad AFR AF: 0.867

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.942 AC: 143388 AN: 152168 Hom.: 67919 Cov.: 30 AF XY: 0.940 AC XY: 69906 AN XY: 74382

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.939

Alfa AF: 0.967 Hom.: 8857

Bravo AF: 0.935

Asia WGS AF: 0.840 AC: 2921 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs167602; hg19: chr11-5561595;