rs5030875

Variant names:

• chr8-66181831-A-C
• rs5030875
• XR_002956713.2:n.240T>G

Variant summary

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

The XR_002956713.2(LOC112268029):​n.240T>G 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 0.0772 in 152,308 control chromosomes in the GnomAD database, including 747 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 0.077 (747 hom., cov: 33)
• Consequence: LOC112268029 XR_002956713.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975
• Publications: 6 publications found

Genes affected

LOC112268029 (HGNC:):

LINC00967 (HGNC:48725): (long intergenic non-protein coding RNA 967)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268029	XR_002956713.2	n.240T>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00967	ENST00000729586.1	n.243+4327A>C		intron_variant	Intron 1 of 3
LINC00967	ENST00000729587.1	n.209+3520A>C		intron_variant	Intron 1 of 3
LINC00967	ENST00000729588.1	n.175+3520A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11714 AN: 152190 Hom.: 745 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0772 AC: 11751 AN: 152308 Hom.: 747 Cov.: 33 AF XY: 0.0752 AC XY: 5601 AN XY: 74470

African (AFR) AF: 0.177 AC: 7344 AN: 41548

American (AMR) AF: 0.0389 AC: 595 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0101 AC: 49 AN: 4828

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0465 AC: 3164 AN: 68024

Other (OTH) AF: 0.0601 AC: 127 AN: 2114

Alfa AF: 0.0933 Hom.: 407

Bravo AF: 0.0820

Asia WGS AF: 0.0270 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.80
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs5030875; hg19: chr8-67094066;