rs741737

chr11-288505-T-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: ENST00000534742.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000534742.1	n.468T>C		non_coding_transcript_exon_variant	1/2	2
	ENST00000525217.1	n.407+13T>C		intron_variant, non_coding_transcript_variant		2

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;