4-188430736-T-C

Variant names:

• chr4-188430736-T-C
• rs907444
• ENST00000512839.5:n.99-5968T>C

Variant summary

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

The ENST00000512839.5(LINC01060):​n.99-5968T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,072 control chromosomes in the GnomAD database, including 5,791 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 0.27 (5791 hom., cov: 32)
• Consequence: LINC01060 ENST00000512839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 1 publications found

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

LOC105377609 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512839.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01060	ENST00000512839.5	TSL:1	n.99-5968T>C		intron	N/A
	LINC01060	ENST00000513313.5	TSL:5	n.99-5968T>C		intron	N/A
	LINC01060	ENST00000806916.1		n.266-5968T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40472 AN: 151954 Hom.: 5786 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.266 AC: 40501 AN: 152072 Hom.: 5791 Cov.: 32 AF XY: 0.264 AC XY: 19658 AN XY: 74338

African (AFR) AF: 0.365 AC: 15141 AN: 41466

American (AMR) AF: 0.231 AC: 3525 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5168

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4822

European-Finnish (FIN) AF: 0.218 AC: 2301 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14681 AN: 67982

Other (OTH) AF: 0.222 AC: 469 AN: 2114

Alfa AF: 0.242 Hom.: 619

Bravo AF: 0.271

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs907444; hg19: chr4-189351890;