rs10837631

Variant names:

• chr11-5225126-T-A
• rs10837631
• ENST00000644706.1:n.336A>T

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: ENSG00000285498 ENST00000644706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

ENSG00000285498 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285498	ENST00000644706.1	n.336A>T		non_coding_transcript_exon_variant	Exon 1 of 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;