rs10494620

Positions:

• chr1-188939929-C-A
• chr1-188939929-C-G
• chr1-188939929-C-T

Variant summary

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

The ENST00000445072.1(LINC01035):​n.239+34003C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 151,888 control chromosomes in the GnomAD database, including 77 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 0.022 (77 hom., cov: 32)
• Consequence: LINC01035 ENST00000445072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805

Genes affected

LINC01035 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01035	NR_174955.1	n.255+34003C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01035	ENST00000445072.1	n.239+34003C>A		intron_variant		3
LINC01035	ENST00000658142.1	n.157+34003C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 3320 AN: 151770 Hom.: 76 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00890

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.0573

Gnomad SAS AF: 0.0535

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00616

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0219 AC: 3329 AN: 151888 Hom.: 77 Cov.: 32 AF XY: 0.0217 AC XY: 1614 AN XY: 74250

Gnomad4 AFR AF: 0.0512

Gnomad4 AMR AF: 0.00888

Gnomad4 ASJ AF: 0.00808

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.0538

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.00616

Gnomad4 OTH AF: 0.0204

Alfa AF: 0.00569 Hom.: 1

Bravo AF: 0.0224

Asia WGS AF: 0.0820 AC: 282 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.038
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494620; hg19: chr1-188909060;