rs10975734

Variant names:

• chr9-6673700-G-A
• rs10975734
• ENST00000687289.2:n.441+3972G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-6673700-G-A
• chr9-6673700-G-C

Variant summary

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

The ENST00000687289.2(LINC02851):​n.441+3972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,792 control chromosomes in the GnomAD database, including 3,969 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 0.22 (3969 hom., cov: 31)
• Consequence: LINC02851 ENST00000687289.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02851	ENST00000687289.2	n.441+3972G>A		intron_variant	Intron 2 of 2
LINC02851	ENST00000813368.1	n.409+3972G>A		intron_variant	Intron 2 of 2
LINC02851	ENST00000813369.1	n.409+3972G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32968 AN: 151674 Hom.: 3971 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.217 AC: 32966 AN: 151792 Hom.: 3969 Cov.: 31 AF XY: 0.210 AC XY: 15558 AN XY: 74198

African (AFR) AF: 0.187 AC: 7712 AN: 41304

American (AMR) AF: 0.183 AC: 2787 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0790 AC: 380 AN: 4808

European-Finnish (FIN) AF: 0.213 AC: 2252 AN: 10572

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17858 AN: 67932

Other (OTH) AF: 0.237 AC: 498 AN: 2100

Alfa AF: 0.251 Hom.: 7589

Bravo AF: 0.217

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.60
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10975734; hg19: chr9-6673700; COSMIC: COSV68726720;