chr15-87431964-T-A

Variant names:

• chr15-87431964-T-A
• rs1822237
• ENST00000656130.2:n.387+1145A>T

Variant summary

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

The NR_187944.1(LOC102724465):​n.310+96A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,100 control chromosomes in the GnomAD database, including 41,705 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 0.73 (41701 hom., cov: 31)
  • Exomes 𝑓: 0.79 (4 hom.)
• Consequence: LOC102724465 NR_187944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802
• Publications: 0 publications found

Genes affected

ENSG00000259560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187944.1. 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
	LOC102724465	NR_187944.1		n.310+96A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259560	ENST00000656130.2		n.387+1145A>T		intron	N/A
	ENSG00000259560	ENST00000665121.1		n.237+1145A>T		intron	N/A
	ENSG00000259560	ENST00000785486.1		n.387+96A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110691 AN: 151968 Hom.: 41632 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.713

GnomAD4 exome AF: 0.786 AC: 11 AN: 14 Hom.: 4 AF XY: 0.833 AC XY: 10 AN XY: 12

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 6 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.729 AC: 110821 AN: 152086 Hom.: 41701 Cov.: 31 AF XY: 0.727 AC XY: 54014 AN XY: 74314

African (AFR) AF: 0.927 AC: 38511 AN: 41524

American (AMR) AF: 0.728 AC: 11125 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3604 AN: 5154

South Asian (SAS) AF: 0.642 AC: 3089 AN: 4808

European-Finnish (FIN) AF: 0.623 AC: 6573 AN: 10556

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43299 AN: 67978

Other (OTH) AF: 0.712 AC: 1502 AN: 2110

Alfa AF: 0.692 Hom.: 4607

Bravo AF: 0.746

Asia WGS AF: 0.700 AC: 2435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1822237; hg19: chr15-87975195;