rs7865244

Variant names:

• chr9-6715730-A-C
• rs7865244
• ENST00000711394.1:n.261-2143A>C

Variant summary

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

The ENST00000711394.1(LINC02851):​n.261-2143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,088 control chromosomes in the GnomAD database, including 26,475 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 0.59 (26475 hom., cov: 33)
• Consequence: LINC02851 ENST00000711394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 3 publications found

Genes affected

LINC02851 (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 (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711394.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02851	ENST00000711394.1		n.261-2143A>C		intron	N/A
	LINC02851	ENST00000813368.1		n.410-2143A>C		intron	N/A
	LINC02851	ENST00000813369.1		n.611-2143A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89283 AN: 151968 Hom.: 26445 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.588 AC: 89358 AN: 152088 Hom.: 26475 Cov.: 33 AF XY: 0.582 AC XY: 43262 AN XY: 74356

African (AFR) AF: 0.655 AC: 27186 AN: 41500

American (AMR) AF: 0.542 AC: 8273 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1954 AN: 5160

South Asian (SAS) AF: 0.552 AC: 2660 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5538 AN: 10576

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39791 AN: 67972

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.586 Hom.: 23846

Bravo AF: 0.590

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.76

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: rs7865244;

hg19: chr9-6715730;