rs11028186

chr11-3574519-A-G

Variant summary

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

The ENST00000710269.1(ENSG00000255367):n.40+6408T>C 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 0.122 in 152,146 control chromosomes in the GnomAD database, including 1,413 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 0.12 (1413 hom., cov: 32)
• Consequence: ENST00000710269.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(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 = 0.173 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
	ENST00000710269.1	n.40+6408T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18580 AN: 152028 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.122 AC: 18588 AN: 152146 Hom.: 1413 Cov.: 32 AF XY: 0.119 AC XY: 8823 AN XY: 74392

Gnomad4 AFR AF: 0.0363

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0518

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.131

Alfa AF: 0.149 Hom.: 337

Bravo AF: 0.120

Asia WGS AF: 0.108 AC: 377 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	0.34
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11028186; hg19: chr11-3595749;