rs1822237

chr15-87431964-T-Achr15-87431964-T-C

Variant summary

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

The ENST00000665121.1(ENSG00000259560):n.237+1145A>T variant causes a intron, non coding transcript 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: ENST00000665121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724465	XR_932586.2	n.321+96A>T		intron_variant, non_coding_transcript_variant
LOC102724465	XR_001751744.2	n.321+96A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665121.1	n.237+1145A>T		intron_variant, non_coding_transcript_variant
	ENST00000656130.1	n.176+1145A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

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

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.712

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.18
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822237; hg19: chr15-87975195;