rs10837631

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000285498 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285498	ENST00000644706.1		n.336A>T		non_coding_transcript_exon	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

African (AFR) AF: 0.193 AC: 328 AN: 1702

American (AMR) AF: 0.270 AC: 1073 AN: 3972

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 586 AN: 2096

East Asian (EAS) AF: 0.308 AC: 1055 AN: 3424

South Asian (SAS) AF: 0.198 AC: 2874 AN: 14482

European-Finnish (FIN) AF: 0.303 AC: 1168 AN: 3858

Middle Eastern (MID) AF: 0.272 AC: 87 AN: 320

European-Non Finnish (NFE) AF: 0.346 AC: 18241 AN: 52706

Other (OTH) AF: 0.318 AC: 1379 AN: 4338

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

African (AFR) AF: 0.201 AC: 8326 AN: 41356

American (AMR) AF: 0.233 AC: 3548 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.324 AC: 1663 AN: 5140

South Asian (SAS) AF: 0.196 AC: 941 AN: 4796

European-Finnish (FIN) AF: 0.321 AC: 3376 AN: 10504

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23129 AN: 67894

Other (OTH) AF: 0.280 AC: 589 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.52
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs10837631; hg19: chr11-5246356;