rs9850953

Positions:

• chr3-30521994-A-G
• chr3-30521994-A-T

Variant summary

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

The ENST00000658053.1(ENSG00000227549):​n.483-13T>C variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,034 control chromosomes in the GnomAD database, including 13,310 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 0.40 (13310 hom., cov: 32)
• Consequence: ENST00000658053.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

LINC01985 (HGNC:52816): (long intergenic non-protein coding RNA 1985)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01985	NR_147054.1	n.91-2713A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01985	ENST00000657930.1	n.126-2709A>G		intron_variant, non_coding_transcript_variant
	ENST00000658053.1	n.483-13T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60128 AN: 151916 Hom.: 13268 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.396 AC: 60221 AN: 152034 Hom.: 13310 Cov.: 32 AF XY: 0.398 AC XY: 29619 AN XY: 74332

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.379

Alfa AF: 0.182 Hom.: 344

Bravo AF: 0.403

Asia WGS AF: 0.452 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9850953; hg19: chr3-30563486;