rs7068008

Variant names:

• chr10-120635798-A-G
• rs7068008
• ENST00000805135.1:n.225A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-120635798-A-G
• chr10-120635798-A-T

Variant summary

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

The ENST00000805135.1(LINC02930):​n.225A>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 0.582 in 152,050 control chromosomes in the GnomAD database, including 26,101 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 0.58 (26101 hom., cov: 32)
• Consequence: LINC02930 ENST00000805135.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 4 publications found

Genes affected

LINC02930 (HGNC:55821): (long intergenic non-protein coding RNA 2930)

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 (AMR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02930	XR_007062314.1	n.852A>G		non_coding_transcript_exon_variant	Exon 1 of 5
LINC02930	XR_002957103.2	n.193-144A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000805135.1	n.225A>G		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02930	ENST00000805137.1	n.225A>G		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02930	ENST00000805139.1	n.229A>G		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88423 AN: 151932 Hom.: 26081 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.582 AC: 88479 AN: 152050 Hom.: 26101 Cov.: 32 AF XY: 0.584 AC XY: 43383 AN XY: 74334

African (AFR) AF: 0.619 AC: 25672 AN: 41468

American (AMR) AF: 0.666 AC: 10172 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3112 AN: 5170

South Asian (SAS) AF: 0.550 AC: 2645 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5751 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36956 AN: 67978

Other (OTH) AF: 0.599 AC: 1266 AN: 2114

Alfa AF: 0.563 Hom.: 81321

Bravo AF: 0.594

Asia WGS AF: 0.552 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.78
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7068008; hg19: chr10-122395310;