11-73995469-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

ENSG00000256723 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000544832.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256723	ENST00000544832.1	TSL:6	n.683G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298594	ENST00000756716.1		n.-74C>T		upstream_gene	N/A

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

African (AFR) AF: 0.286 AC: 84 AN: 294

American (AMR) AF: 0.341 AC: 144 AN: 422

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 50 AN: 268

East Asian (EAS) AF: 0.206 AC: 127 AN: 618

South Asian (SAS) AF: 0.218 AC: 489 AN: 2238

European-Finnish (FIN) AF: 0.215 AC: 377 AN: 1752

Middle Eastern (MID) AF: 0.342 AC: 26 AN: 76

European-Non Finnish (NFE) AF: 0.239 AC: 3300 AN: 13796

Other (OTH) AF: 0.206 AC: 212 AN: 1028

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

African (AFR) AF: 0.306 AC: 12700 AN: 41472

American (AMR) AF: 0.322 AC: 4914 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.147 AC: 761 AN: 5174

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4818

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10580

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16654 AN: 67980

Other (OTH) AF: 0.255 AC: 536 AN: 2106

Alfa AF: 0.251 Hom.: 10288

Bravo AF: 0.274

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.8
DANN	Benign	0.77
PhyloP100		0.047

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs668514;

hg19: chr11-73706514;