rs7904001

Variant names:

• chr10-65002965-G-A
• rs7904001
• ENST00000655566.1:n.89-2715C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-65002965-G-A
• chr10-65002965-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655566.1(LINC02671):​n.89-2715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,858 control chromosomes in the GnomAD database, including 7,842 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 0.32 (7842 hom., cov: 33)
• Consequence: LINC02671 ENST00000655566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

Genes affected

LINC02671 (HGNC:54158): (long intergenic non-protein coding RNA 2671)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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
LINC02671	ENST00000655566.1	n.89-2715C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47984 AN: 151740 Hom.: 7840 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.316 AC: 48008 AN: 151858 Hom.: 7842 Cov.: 33 AF XY: 0.319 AC XY: 23654 AN XY: 74214

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.319

Alfa AF: 0.301 Hom.: 1136

Bravo AF: 0.312

Asia WGS AF: 0.267 AC: 924 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7904001; hg19: chr10-66762723;