rs1869454

Positions:

• chr15-48001252-C-T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.251+8481C>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 0.0488 in 152,222 control chromosomes in the GnomAD database, including 488 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 0.049 (488 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900354	XR_001751516.3	n.205+8481C>T		intron_variant, non_coding_transcript_variant
LOC102724553	XR_001751520.2	n.262+1456G>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.145+8481C>T		intron_variant, non_coding_transcript_variant
LOC102724553	XR_001751521.2	n.262+1456G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662551.1	n.251+8481C>T		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.258+8481C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000664705.1	n.319+3097C>T		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.220+3097C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7397 AN: 152104 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000647

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0488 AC: 7433 AN: 152222 Hom.: 488 Cov.: 32 AF XY: 0.0490 AC XY: 3649 AN XY: 74412

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0873

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.000647

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0169 Hom.: 167

Bravo AF: 0.0595

Asia WGS AF: 0.0670 AC: 235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869454; hg19: chr15-48293449;