rs1369822

Positions:

• chr12-95805840-T-C

Variant summary

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

The NR_135014.1(SNRPF-DT):​n.155-10183A>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 0.633 in 152,030 control chromosomes in the GnomAD database, including 32,390 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 0.63 (32390 hom., cov: 31)
• Consequence: SNRPF-DT NR_135014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LINC02410 (HGNC:53339): (long intergenic non-protein coding RNA 2410)

SNRPF-DT (HGNC:55452): (SNRPF divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNRPF-DT	NR_135014.1	n.155-10183A>G		intron_variant, non_coding_transcript_variant
LINC02410	NR_135016.1	n.174+2570T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02410	ENST00000553095.1	n.174+2570T>C		intron_variant, non_coding_transcript_variant		2
SNRPF-DT	ENST00000670743.1	n.142-10183A>G		intron_variant, non_coding_transcript_variant
SNRPF-DT	ENST00000553194.1	n.155-10183A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96112 AN: 151912 Hom.: 32333 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.633 AC: 96222 AN: 152030 Hom.: 32390 Cov.: 31 AF XY: 0.639 AC XY: 47494 AN XY: 74290

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.612

Alfa AF: 0.535 Hom.: 11480

Bravo AF: 0.641

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369822; hg19: chr12-96199618;