rs1745903

Variant names:

• chr10-86992449-G-A
• rs1745903
• ENST00000444431.1:n.44G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444431.1(ENSG00000151303):​n.44G>A 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 0.372 in 236,584 control chromosomes in the GnomAD database, including 17,830 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 0.39 (12730 hom., cov: 32)
  • Exomes 𝑓: 0.33 (5100 hom.)
• Consequence: ENSG00000151303 ENST00000444431.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38
• Publications: 5 publications found

Genes affected

ENSG00000151303 (HGNC:):

BMS1P3 (HGNC:23651): (BMS1 pseudogene 3)

ADIRF (HGNC:24043): (adipogenesis regulatory factor) APM2 gene is exclusively expressed in adipose tissue. Its function is currently unknown. [provided by RefSeq, Jul 2008]

AGAP11 (HGNC:29421): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 11) Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444431.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGAP11	NR_171046.1		n.871G>A		non_coding_transcript_exon	Exon 3 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000151303	ENST00000444431.1	TSL:1	n.44G>A		non_coding_transcript_exon	Exon 1 of 7
	BMS1P3	ENST00000372011.4	TSL:6	n.197G>A		non_coding_transcript_exon	Exon 1 of 6
	ENSG00000151303	ENST00000433214.2	TSL:2	n.567G>A		non_coding_transcript_exon	Exon 4 of 12

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59966 AN: 151972 Hom.: 12701 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.374

GnomAD4 exome AF: 0.331 AC: 27935 AN: 84494 Hom.: 5100 Cov.: 0 AF XY: 0.327 AC XY: 15733 AN XY: 48106

African (AFR) AF: 0.535 AC: 1094 AN: 2046

American (AMR) AF: 0.558 AC: 4996 AN: 8946

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 422 AN: 1180

East Asian (EAS) AF: 0.218 AC: 1139 AN: 5216

South Asian (SAS) AF: 0.329 AC: 2577 AN: 7828

European-Finnish (FIN) AF: 0.278 AC: 4499 AN: 16168

Middle Eastern (MID) AF: 0.391 AC: 647 AN: 1654

European-Non Finnish (NFE) AF: 0.302 AC: 11559 AN: 38244

Other (OTH) AF: 0.312 AC: 1002 AN: 3212

GnomAD4 genome AF: 0.395 AC: 60035 AN: 152090 Hom.: 12730 Cov.: 32 AF XY: 0.394 AC XY: 29274 AN XY: 74370

African (AFR) AF: 0.535 AC: 22174 AN: 41460

American (AMR) AF: 0.475 AC: 7261 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3466

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5184

South Asian (SAS) AF: 0.346 AC: 1670 AN: 4820

European-Finnish (FIN) AF: 0.305 AC: 3233 AN: 10588

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22000 AN: 67976

Other (OTH) AF: 0.373 AC: 784 AN: 2104

Alfa AF: 0.387 Hom.: 1745

Bravo AF: 0.412

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	4.3
DANN	Benign	0.33
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs1745903; hg19: chr10-88752206;