chr9-129495504-C-T

Position:

• chr9-129495504-C-T

Variant summary

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

The XM_047424328.1(LOC124900275):​c.*225+1909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,158 control chromosomes in the GnomAD database, including 10,726 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 0.35 (10721 hom., cov: 33)
  • Exomes 𝑓: 0.45 (5 hom.)
• Consequence: LOC124900275 XM_047424328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

LOC124900275 (HGNC:):

LINC00963 (HGNC:48716): (long intergenic non-protein coding RNA 963)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900275	XM_047424328.1	c.*225+1909C>T		intron_variant			XP_047280284.1
LINC00963	NR_038955.1	n.758+1909C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00963	ENST00000653047.1	n.305+6205C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52512 AN: 151998 Hom.: 10728 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.452 AC: 19 AN: 42 Hom.: 5 Cov.: 0 AF XY: 0.441 AC XY: 15 AN XY: 34

Gnomad4 AFR exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.345 AC: 52509 AN: 152116 Hom.: 10721 Cov.: 33 AF XY: 0.346 AC XY: 25712 AN XY: 74340

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.347

Alfa AF: 0.436 Hom.: 19545

Bravo AF: 0.333

Asia WGS AF: 0.339 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.79
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: rs1220789; hg19: chr9-132257783;