9-3198250-C-A

Variant names:

• chr9-3198250-C-A
• rs1407379
• ENST00000452746.1:n.619C>A

Variant summary

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

The ENST00000659476.1(LINC01231):​n.1050+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,114 control chromosomes in the GnomAD database, including 4,711 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 0.23 (4711 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC01231 ENST00000659476.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 1 publications found

Genes affected

LINC01231 (HGNC:49688): (long intergenic non-protein coding RNA 1231)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659476.1. 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
	LINC01231	NR_121585.1		n.619C>A		non_coding_transcript_exon	Exon 4 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01231	ENST00000452746.1	TSL:3	n.619C>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01231	ENST00000654614.2		n.569C>A		non_coding_transcript_exon	Exon 3 of 4
	LINC01231	ENST00000663825.1		n.748C>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34774 AN: 151996 Hom.: 4706 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.248

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.229 AC: 34798 AN: 152114 Hom.: 4711 Cov.: 33 AF XY: 0.232 AC XY: 17221 AN XY: 74356

African (AFR) AF: 0.336 AC: 13932 AN: 41488

American (AMR) AF: 0.265 AC: 4056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2462 AN: 5166

South Asian (SAS) AF: 0.206 AC: 991 AN: 4814

European-Finnish (FIN) AF: 0.169 AC: 1794 AN: 10588

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 10020 AN: 67992

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.175 Hom.: 1465

Bravo AF: 0.246

Asia WGS AF: 0.308 AC: 1070 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.90
DANN	Benign	0.45
PhyloP100		0.011

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1407379;

hg19: chr9-3198250;