chr9-129495504-C-T

Variant names:

• chr9-129495504-C-T
• rs1220789
• ENST00000412141.2:n.203+1909C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607931.1(LINC00963):​n.60C>T variant causes a non coding transcript exon 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: LINC00963 ENST00000607931.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 7 publications found

Genes affected

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

LOC124900275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607931.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00963	NR_038955.1		n.758+1909C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00963	ENST00000412141.2	TSL:1	n.203+1909C>T		intron	N/A
	LINC00963	ENST00000419300.3	TSL:1	n.200+6205C>T		intron	N/A
	LINC00963	ENST00000444184.7	TSL:1	n.935+1909C>T		intron	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.406 AC: 13 AN: 32

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.114 AC: 4724 AN: 41544

American (AMR) AF: 0.400 AC: 6113 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1743 AN: 5164

South Asian (SAS) AF: 0.427 AC: 2056 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4080 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30911 AN: 67950

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.426 Hom.: 23897

Bravo AF: 0.333

Asia WGS AF: 0.339 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.79
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1220789; hg19: chr9-132257783;