1-185619352-T-G

Position:

• chr1-185619352-T-G

Variant summary

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

The ENST00000608417.6(LINC01350):​n.166+7140A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,224 control chromosomes in the GnomAD database, including 687 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 0.064 (687 hom., cov: 31)
• Consequence: LINC01350 ENST00000608417.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

LINC01350 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01350	NR_110793.1	n.146+7140A>C		intron_variant
LOC107985239	XR_001738340.2	n.1067-60097T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01350	ENST00000608417.6	n.166+7140A>C		intron_variant		1
LINC01350	ENST00000436955.1	n.424+2109A>C		intron_variant		3
LINC01350	ENST00000439633.7	n.151+7140A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9663 AN: 152108 Hom.: 680 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00916

Gnomad OTH AF: 0.0501

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

GnomAD4 genome AF: 0.0637 AC: 9692 AN: 152224 Hom.: 687 Cov.: 31 AF XY: 0.0669 AC XY: 4975 AN XY: 74418

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.00916

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0192 Hom.: 206

Bravo AF: 0.0711

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073470; hg19: chr1-185588484;