rs1861896

chr2-185737324-C-T

Variant summary

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

The NR_110217.1(FSIP2-AS2):n.99+3055G>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 0.322 in 152,018 control chromosomes in the GnomAD database, including 8,131 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 0.32 (8131 hom., cov: 32)
• Consequence: FSIP2-AS2 NR_110217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

FSIP2-AS2 (HGNC:54061): (FSIP2 antisense RNA 2)

FSIP2-AS1 (HGNC:40978): (FSIP2 antisense RNA 1)

FSIP2 (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 = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSIP2-AS2	NR_110217.1	n.99+3055G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSIP2-AS2	ENST00000421998.5	n.153-1192G>A		intron_variant, non_coding_transcript_variant		1
FSIP2-AS2	ENST00000427269.2	n.101+3055G>A		intron_variant, non_coding_transcript_variant		5
FSIP2-AS1	ENST00000667756.1	n.37+51442G>A		intron_variant, non_coding_transcript_variant
FSIP2-AS2	ENST00000437717.1	n.187+862G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48997 AN: 151902 Hom.: 8132 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.322 AC: 48997 AN: 152018 Hom.: 8131 Cov.: 32 AF XY: 0.316 AC XY: 23490 AN XY: 74312

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.352

Alfa AF: 0.328 Hom.: 1312

Bravo AF: 0.333

Asia WGS AF: 0.296 AC: 1033 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	0.68
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861896; hg19: chr2-186602051;