rs9640883

Variant names:

• chr7-134431881-G-A
• rs9640883
• ENST00000607945.2: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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609619.3(LINC03060):​n.187+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 ENST00000609619.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 10 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609619.3. 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
	LINC03060	NR_183388.1		n.107+433C>T		intron	N/A
	LINC03060	NR_183389.1		n.107+433C>T		intron	N/A
	LINC03060	NR_183390.1		n.107+433C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03060	ENST00000607945.2	TSL:4	n.118+433C>T		intron	N/A
	LINC03060	ENST00000609209.2	TSL:5	n.123+433C>T		intron	N/A
	LINC03060	ENST00000609619.3	TSL:2	n.187+433C>T		intron	N/A

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

African (AFR) AF: 0.0549 AC: 2278 AN: 41526

American (AMR) AF: 0.341 AC: 5203 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3053 AN: 5132

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4808

European-Finnish (FIN) AF: 0.268 AC: 2829 AN: 10552

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17263 AN: 67992

Other (OTH) AF: 0.227 AC: 481 AN: 2116

Alfa AF: 0.232 Hom.: 4913

Bravo AF: 0.221

Asia WGS AF: 0.376 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.19

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: rs9640883;

hg19: chr7-134116633;