rs9640883

Variant names:

• chr7-134431881-G-A
• rs9640883
• ENST00000607945.1:n.118+433C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-134431881-G-A
• chr7-134431881-G-C

Variant summary

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

The ENST00000609619.2(LINC03060):​n.172+433C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,074 control chromosomes in the GnomAD database, including 4,951 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 (4951 hom., cov: 32)
• Consequence: LINC03060 ENST00000609619.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

Genes affected

LINC03060 (HGNC:56367): (long intergenic non-protein coding RNA 3060)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03060	NR_183388.1	n.107+433C>T		intron_variant	Intron 1 of 1
LINC03060	NR_183389.1	n.107+433C>T		intron_variant	Intron 1 of 4
LINC03060	NR_183390.1	n.107+433C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03060	ENST00000607945.1	n.118+433C>T		intron_variant	Intron 1 of 2	4
LINC03060	ENST00000609209.1	n.103+433C>T		intron_variant	Intron 1 of 2	5
LINC03060	ENST00000609619.2	n.172+433C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33698 AN: 151956 Hom.: 4945 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.222 AC: 33709 AN: 152074 Hom.: 4951 Cov.: 32 AF XY: 0.227 AC XY: 16860 AN XY: 74318

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.227

Alfa AF: 0.248 Hom.: 2687

Bravo AF: 0.221

Asia WGS AF: 0.376 AC: 1302 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	5.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9640883; hg19: chr7-134116633;