rs907444

chr4-188430736-T-C

Variant summary

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

The XR_001741960.2(LOC105377609):n.4747A>G variant causes a non coding transcript exon 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: LOC105377609 XR_001741960.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

Genes affected

LOC105377609 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377609	XR_001741960.2	n.4747A>G		non_coding_transcript_exon_variant	4/4
LOC105377609	XR_939621.3	n.4735A>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01060	ENST00000512839.5	n.99-5968T>C		intron_variant, non_coding_transcript_variant		1
LINC01060	ENST00000513313.5	n.99-5968T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.222

Alfa AF: 0.236 Hom.: 562

Bravo AF: 0.271

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907444; hg19: chr4-189351890;