rs741737

Variant names:

• chr11-288505-T-C
• rs741737
• ENST00000534742.1:n.468T>C

Variant summary

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

The ENST00000534742.1(ENSG00000255026):​n.468T>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 0.184 in 152,366 control chromosomes in the GnomAD database, including 3,208 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 0.18 (3203 hom., cov: 33)
  • Exomes 𝑓: 0.28 (5 hom.)
• Consequence: ENSG00000255026 ENST00000534742.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

ENSG00000255026 (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 (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255026	ENST00000534742.1	n.468T>C		non_coding_transcript_exon_variant	Exon 1 of 2	2
ENSG00000255026	ENST00000525217.1	n.407+13T>C		intron_variant	Intron 1 of 2	2
ENSG00000255026	ENST00000533924.1	n.*207T>C		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27920 AN: 152074 Hom.: 3206 Cov.: 33

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.282 AC: 49 AN: 174 Hom.: 5 Cov.: 0 AF XY: 0.303 AC XY: 40 AN XY: 132

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.200

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.183 AC: 27913 AN: 152192 Hom.: 3203 Cov.: 33 AF XY: 0.184 AC XY: 13718 AN XY: 74406

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.173

Alfa AF: 0.218 Hom.: 1074

Bravo AF: 0.169

Asia WGS AF: 0.0640 AC: 226 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	7.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs741737; hg19: chr11-288505; COSMIC: COSV56461280;