rs10493083

Variant names:

• chr1-38486496-T-C
• rs10493083
• ENST00000634298.1:n.909-9335T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-38486496-T-C
• chr1-38486496-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634298.1(LINC01685):​n.909-9335T>C variant causes a intron 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 ENST00000634298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 4 publications found

Genes affected

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

LOC105378657 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105378657	XR_947210.3	n.424+13500A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01685	ENST00000634298.1	n.909-9335T>C		intron_variant	Intron 1 of 1	5
LINC01685	ENST00000634464.2	n.950-7075T>C		intron_variant	Intron 1 of 2	5
LINC01685	ENST00000654266.1	n.935+10672T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.408 AC: 16902 AN: 41458

American (AMR) AF: 0.121 AC: 1859 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5180

South Asian (SAS) AF: 0.102 AC: 493 AN: 4828

European-Finnish (FIN) AF: 0.0383 AC: 406 AN: 10614

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1146 AN: 68020

Other (OTH) AF: 0.115 AC: 243 AN: 2116

Alfa AF: 0.0486 Hom.: 1348

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10493083; hg19: chr1-38952168;