rs2899383

Positions:

• chr15-45804853-A-G

Variant summary

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

The NR_135680.1(LOC105370802):​n.96-43728A>G 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 0.613 in 152,060 control chromosomes in the GnomAD database, including 28,982 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 0.61 (28982 hom., cov: 32)
• Consequence: LOC105370802 NR_135680.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370802	NR_135680.1	n.96-43728A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559600.1	n.96-43728A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000560705.1	n.556+12938A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93223 AN: 151942 Hom.: 28957 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.613 AC: 93288 AN: 152060 Hom.: 28982 Cov.: 32 AF XY: 0.616 AC XY: 45794 AN XY: 74334

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.624

Alfa AF: 0.611 Hom.: 4822

Bravo AF: 0.596

Asia WGS AF: 0.676 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2899383; hg19: chr15-46097051;