chr9-115904263-T-A

Variant names:

• chr9-115904263-T-A
• rs971037
• ENST00000374014.4:n.701+108A>T

Variant summary

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

The ENST00000832547.1(LINC00474):​n.593A>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 0.451 in 152,088 control chromosomes in the GnomAD database, including 16,156 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 0.45 (16124 hom., cov: 32)
  • Exomes 𝑓: 0.49 (32 hom.)
• Consequence: LINC00474 ENST00000832547.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 1 publications found

Genes affected

LINC00474 (HGNC:23367): (long intergenic non-protein coding RNA 474)

ENSG00000308189 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832547.1. 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
	LINC00474	NR_024032.2		n.457+108A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00474	ENST00000374014.4	TSL:1	n.701+108A>T		intron	N/A
	LINC00474	ENST00000832547.1		n.593A>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00474	ENST00000832548.1		n.487A>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68397 AN: 151702 Hom.: 16122 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.489 AC: 131 AN: 268 Hom.: 32 AF XY: 0.506 AC XY: 87 AN XY: 172

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.489 AC: 128 AN: 262

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.451 AC: 68431 AN: 151820 Hom.: 16124 Cov.: 32 AF XY: 0.451 AC XY: 33432 AN XY: 74178

African (AFR) AF: 0.322 AC: 13358 AN: 41440

American (AMR) AF: 0.417 AC: 6351 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2295 AN: 5138

South Asian (SAS) AF: 0.500 AC: 2411 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5608 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35260 AN: 67842

Other (OTH) AF: 0.453 AC: 957 AN: 2112

Alfa AF: 0.376 Hom.: 1147

Bravo AF: 0.434

Asia WGS AF: 0.428 AC: 1487 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.32
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs971037; hg19: chr9-118666542;