rs12324326

Positions:

• chr15-47855938-C-T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+43022C>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 0.122 in 152,016 control chromosomes in the GnomAD database, including 1,378 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 0.12 (1378 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000662551.1	n.188+43022C>T		intron_variant, non_coding_transcript_variant
	ENST00000664705.1	n.188+43022C>T		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.68+43022C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18491 AN: 151898 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.122 AC: 18505 AN: 152016 Hom.: 1378 Cov.: 32 AF XY: 0.126 AC XY: 9323 AN XY: 74282

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.114

Alfa AF: 0.102 Hom.: 807

Bravo AF: 0.120

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12324326; hg19: chr15-48148135;