rs10493083

chr1-38486496-T-Cchr1-38486496-T-G

Variant summary

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

The ENST00000658172.1(LINC01685):n.943+10672T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,198 control chromosomes in the GnomAD database, including 3,747 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 0.15 (3747 hom., cov: 32)
• Consequence: LINC01685 ENST00000658172.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

LINC01685 (HGNC:52473): (long intergenic non-protein coding RNA 1685)

LOC105378657 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378657	XR_947210.3	n.424+13500A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01685	ENST00000658172.1	n.943+10672T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22144 AN: 152078 Hom.: 3727 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.146 AC: 22222 AN: 152198 Hom.: 3747 Cov.: 32 AF XY: 0.147 AC XY: 10932 AN XY: 74432

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0383

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0694 Hom.: 605

Bravo AF: 0.164

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493083; hg19: chr1-38952168;