chr9-22695594-A-T

Variant names:

• chr9-22695594-A-T
• rs976731
• XR_001746635.2:n.11164T>A

Variant summary

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

The XR_001746635.2(LOC107987054):​n.11164T>A 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 0.746 in 151,562 control chromosomes in the GnomAD database, including 42,744 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 0.75 (42744 hom., cov: 33)
• Consequence: LOC107987054 XR_001746635.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 3 publications found

Genes affected

LOC107987054 (HGNC:):

LINC01239 (HGNC:49796): (long intergenic non-protein coding RNA 1239)

ENSG00000284418 (HGNC:58153):

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 (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987054	XR_001746635.2	n.11164T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC01239	NR_038977.1	n.402+12881A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01239	ENST00000436786.2	n.500+12881A>T		intron_variant	Intron 3 of 5	2
ENSG00000284418	ENST00000764217.1	n.384-4937T>A		intron_variant	Intron 3 of 5
ENSG00000284418	ENST00000764218.1	n.384-22960T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.746 AC: 112905 AN: 151444 Hom.: 42704 Cov.: 33

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.763

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.746 AC: 113004 AN: 151562 Hom.: 42744 Cov.: 33 AF XY: 0.739 AC XY: 54708 AN XY: 74052

African (AFR) AF: 0.874 AC: 36242 AN: 41456

American (AMR) AF: 0.751 AC: 11390 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2519 AN: 3462

East Asian (EAS) AF: 0.608 AC: 3121 AN: 5132

South Asian (SAS) AF: 0.693 AC: 3338 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6207 AN: 10546

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47789 AN: 67670

Other (OTH) AF: 0.764 AC: 1608 AN: 2104

Alfa AF: 0.726 Hom.: 5038

Bravo AF: 0.761

Asia WGS AF: 0.694 AC: 2412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs976731; hg19: chr9-22695593;