rs907444

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 XR_939621.3(LOC105377609):​n.4735A>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_939621.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377609	XR_001741960.2	n.4747A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105377609	XR_939621.3	n.4735A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000512839.5	n.99-5968T>C		intron_variant	Intron 1 of 4	1
LINC01060	ENST00000513313.5	n.99-5968T>C		intron_variant	Intron 1 of 2	5
LINC01060	ENST00000806916.1	n.266-5968T>C		intron_variant	Intron 1 of 4

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 v4.3

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

Publications

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Other links and lift over

dbSNP: rs907444; hg19: chr4-189351890;