chr2-19869619-C-A

Position:

• chr2-19869619-C-A

Variant summary

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

The NR_033875.1(LINC00954):​n.217+6C>A variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,362 control chromosomes in the GnomAD database, including 2,894 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 0.18 (2890 hom., cov: 33)
  • Exomes 𝑓: 0.19 (4 hom.)
• Consequence: LINC00954 NR_033875.1 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

LINC00954 (HGNC:48668): (long intergenic non-protein coding RNA 954)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00954	NR_033875.1	n.217+6C>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00954	ENST00000449086.5	n.197+6C>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		1
LINC00954	ENST00000433669.2	n.197+6C>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		2
LINC00954	ENST00000456119.5	n.262+6C>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		4
LINC00954	ENST00000607100.5	n.211+6C>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27901 AN: 152072 Hom.: 2887 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.192 AC: 33 AN: 172 Hom.: 4 Cov.: 0 AF XY: 0.216 AC XY: 29 AN XY: 134

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.194

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.184 AC: 27929 AN: 152190 Hom.: 2890 Cov.: 33 AF XY: 0.184 AC XY: 13719 AN XY: 74406

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.185

Alfa AF: 0.144 Hom.: 2238

Bravo AF: 0.194

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2276607; hg19: chr2-20069380;