rs1240373

Variant names:

• chr10-87000265-C-G
• rs1240373
• ENST00000444431.1:n.1152C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-87000265-C-G
• chr10-87000265-C-T

Variant summary

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

The ENST00000444431.1(ENSG00000151303):​n.1152C>G 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 0.348 in 1,021,504 control chromosomes in the GnomAD database, including 66,073 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 0.43 (15655 hom., cov: 32)
  • Exomes 𝑓: 0.33 (50418 hom.)
• Consequence: ENSG00000151303 ENST00000444431.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

ENSG00000151303 (HGNC:):

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

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMS1P3		n.87000265C>G		intragenic_variant
AGAP11	NR_171046.1	n.1306-54C>G		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000151303	ENST00000444431.1	n.1152C>G		non_coding_transcript_exon_variant	Exon 4 of 7	1
BMS1P3	ENST00000372011.4	n.816-54C>G		intron_variant	Intron 5 of 5	6
ENSG00000271880	ENST00000433214.2	n.1002-54C>G		intron_variant	Intron 7 of 11	2
ENSG00000272508	ENST00000444180.3	n.345-54C>G		intron_variant	Intron 3 of 9	2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65459 AN: 151826 Hom.: 15617 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.333 AC: 289761 AN: 869560 Hom.: 50418 Cov.: 11 AF XY: 0.335 AC XY: 143952 AN XY: 430108

Gnomad4 AFR exome AF: 0.646

Gnomad4 AMR exome AF: 0.554

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.235

Gnomad4 SAS exome AF: 0.352

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.345

GnomAD4 genome AF: 0.431 AC: 65543 AN: 151944 Hom.: 15655 Cov.: 32 AF XY: 0.428 AC XY: 31824 AN XY: 74270

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.401

Alfa AF: 0.216 Hom.: 436

Bravo AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1240373; hg19: chr10-88760022; COSMIC: COSV64393547;