11-73995469-C-T

Variant names:

• chr11-73995469-C-T
• rs668514
• ENST00000544832.1:n.683G>A

Variant summary

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

The ENST00000544832.1(ENSG00000256723):​n.683G>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 0.259 in 172,578 control chromosomes in the GnomAD database, including 6,066 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 0.26 (5450 hom., cov: 33)
  • Exomes 𝑓: 0.23 (616 hom.)
• Consequence: ENSG00000256723 ENST00000544832.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

ENSG00000256723 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100421622		n.73995469C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256723	ENST00000544832.1	n.683G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39850 AN: 151968 Hom.: 5451 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.235 AC: 4809 AN: 20492 Hom.: 616 Cov.: 0 AF XY: 0.229 AC XY: 3228 AN XY: 14096

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.341

Gnomad4 ASJ exome AF: 0.187

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.218

Gnomad4 FIN exome AF: 0.215

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.262 AC: 39860 AN: 152086 Hom.: 5450 Cov.: 33 AF XY: 0.260 AC XY: 19333 AN XY: 74322

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.255

Alfa AF: 0.250 Hom.: 2644

Bravo AF: 0.274

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs668514; hg19: chr11-73706514;