chr11-5540365-C-T

Variant names:

• chr11-5540365-C-T
• rs167602
• ENST00000380259.7:n.*739+50460G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+50460G>A		intron_variant	Intron 5 of 7	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;