rs12594966

Positions:

• chr15-48027774-C-T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.252-21016C>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 0.0214 in 152,274 control chromosomes in the GnomAD database, including 336 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 0.021 (336 hom., cov: 33)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900354	XR_001751516.3	n.206-21016C>T		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.146-21016C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662551.1	n.252-21016C>T		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.259-21016C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000665188.1	n.221-21063C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3268 AN: 152156 Hom.: 338 Cov.: 33

Gnomad AFR AF: 0.00645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00654

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0214 AC: 3264 AN: 152274 Hom.: 336 Cov.: 33 AF XY: 0.0235 AC XY: 1750 AN XY: 74460

Gnomad4 AFR AF: 0.00643

Gnomad4 AMR AF: 0.0299

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.00654

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0101 Hom.: 14

Bravo AF: 0.0230

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12594966; hg19: chr15-48319971;