rs10160399

chr11-4495346-C-T

Variant summary

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

The ENST00000690302.1(ENSG00000291144):n.380-24317C>T 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 0.103 in 152,142 control chromosomes in the GnomAD database, including 1,161 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 0.10 (1161 hom., cov: 32)
• Consequence: ENST00000690302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690302.1	n.380-24317C>T		intron_variant, non_coding_transcript_variant
	ENST00000685350.1	n.541-24317C>T		intron_variant, non_coding_transcript_variant
	ENST00000691418.1	n.366-23401C>T		intron_variant, non_coding_transcript_variant
	ENST00000693118.1	n.366-8762C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15659 AN: 152024 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.103 AC: 15718 AN: 152142 Hom.: 1161 Cov.: 32 AF XY: 0.101 AC XY: 7524 AN XY: 74370

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0664

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0875

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.100 Hom.: 103

Bravo AF: 0.113

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.63
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10160399; hg19: chr11-4516576;