chr11-4393849-T-C

Position:

• chr11-4393849-T-C

Variant summary

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

The ENST00000690302.1(ENSG00000291144):​n.63T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,920 control chromosomes in the GnomAD database, including 3,271 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 0.20 (3271 hom., cov: 31)
• Consequence: ENST00000690302.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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.63T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30172 AN: 151802 Hom.: 3269 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.199 AC: 30179 AN: 151920 Hom.: 3271 Cov.: 31 AF XY: 0.196 AC XY: 14572 AN XY: 74288

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.208

Alfa AF: 0.191 Hom.: 5260

Bravo AF: 0.201

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11032080; hg19: chr11-4415079;