rs11235965

Positions:

• chr11-73995246-C-T

Variant summary

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

The ENST00000544832.1(ENSG00000256723):​n.906G>A 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 0.223 in 156,904 control chromosomes in the GnomAD database, including 4,236 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 0.22 (4029 hom., cov: 32)
  • Exomes 𝑓: 0.29 (207 hom.)
• Consequence: ENST00000544832.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000544832.1	n.906G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33514 AN: 151948 Hom.: 4032 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.289 AC: 1399 AN: 4836 Hom.: 207 Cov.: 0 AF XY: 0.280 AC XY: 891 AN XY: 3180

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.387

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.252

GnomAD4 genome AF: 0.220 AC: 33516 AN: 152068 Hom.: 4029 Cov.: 32 AF XY: 0.225 AC XY: 16752 AN XY: 74318

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.184

Alfa AF: 0.227 Hom.: 676

Bravo AF: 0.197

Asia WGS AF: 0.246 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11235965; hg19: chr11-73706291;