rs2460641

chr15-45833571-A-Cchr15-45833571-A-Gchr15-45833571-A-T

Variant summary

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

The NR_135680.1(LOC105370802):n.96-15010A>C 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 0.369 in 151,888 control chromosomes in the GnomAD database, including 10,911 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 0.37 (10911 hom., cov: 31)
• Consequence: LOC105370802 NR_135680.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370802	NR_135680.1	n.96-15010A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559600.1	n.96-15010A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000560705.1	n.557-15010A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56058 AN: 151770 Hom.: 10899 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.369 AC: 56112 AN: 151888 Hom.: 10911 Cov.: 31 AF XY: 0.373 AC XY: 27695 AN XY: 74228

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.358

Alfa AF: 0.306 Hom.: 10862

Bravo AF: 0.384

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	5.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2460641; hg19: chr15-46125769;