rs1450418

chr15-36874677-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_024264.1(LOC145845):n.687+1683G>A 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 0.675 in 152,050 control chromosomes in the GnomAD database, including 35,137 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 0.67 (35137 hom., cov: 33)
• Consequence: LOC145845 NR_024264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC145845	NR_024264.1	n.687+1683G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690156.1	n.385+1683G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102514 AN: 151932 Hom.: 35110 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.675 AC: 102595 AN: 152050 Hom.: 35137 Cov.: 33 AF XY: 0.678 AC XY: 50433 AN XY: 74332

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.703

Alfa AF: 0.707 Hom.: 76424

Bravo AF: 0.678

Asia WGS AF: 0.706 AC: 2455 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	16
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450418; hg19: chr15-37166878;