rs1856591

chr10-45103170-C-T

Variant summary

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

The NR_024472.1(RSU1P2):n.821-2671G>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 0.507 in 151,968 control chromosomes in the GnomAD database, including 19,778 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 0.51 (19778 hom., cov: 32)
• Consequence: RSU1P2 NR_024472.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1P2	NR_024472.1	n.821-2671G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000448600.5	n.570-2671G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000619977.1	n.821-2671G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000661630.1	n.508-2709G>A		intron_variant, non_coding_transcript_variant
	ENST00000423875.1	n.1374-2671G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76931 AN: 151850 Hom.: 19764 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.507 AC: 76988 AN: 151968 Hom.: 19778 Cov.: 32 AF XY: 0.511 AC XY: 37926 AN XY: 74288

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.490

Alfa AF: 0.518 Hom.: 42118

Bravo AF: 0.510

Asia WGS AF: 0.445 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856591; hg19: chr10-45598618;