rs10837631

chr11-5225126-T-A

Variant summary

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

The ENST00000644706.1(ENSG00000285498):n.336A>T 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 0.293 in 238,600 control chromosomes in the GnomAD database, including 10,973 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 0.28 (6574 hom., cov: 32)
  • Exomes 𝑓: 0.31 (4399 hom.)
• Consequence: ENST00000644706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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
	ENST00000644706.1	n.336A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43164 AN: 151582 Hom.: 6571 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.308 AC: 26791 AN: 86898 Hom.: 4399 Cov.: 0 AF XY: 0.297 AC XY: 13824 AN XY: 46512

Gnomad4 AFR exome AF: 0.193

Gnomad4 AMR exome AF: 0.270

Gnomad4 ASJ exome AF: 0.280

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.303

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.318

GnomAD4 genome AF: 0.285 AC: 43186 AN: 151702 Hom.: 6574 Cov.: 32 AF XY: 0.282 AC XY: 20935 AN XY: 74142

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.280

Alfa AF: 0.302 Hom.: 886

Bravo AF: 0.279

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.5
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837631; hg19: chr11-5246356;