rs17055893

Variant names:

• chr13-37489491-A-C
• rs17055893
• ENST00000827669.1:n.322-936A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-37489491-A-C
• chr13-37489491-A-G

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.322-936A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0789 in 152,136 control chromosomes in the GnomAD database, including 1,138 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 0.079 (1138 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 1 publications found

Genes affected

ENSG00000307651 (HGNC:):

LINC01048 (HGNC:49042): (long intergenic non-protein coding RNA 1048)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903159	XR_007063761.1	n.343-936A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307651	ENST00000827669.1	n.322-936A>C		intron_variant	Intron 3 of 3
LINC01048	ENST00000827904.1	n.103-5098T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11972 AN: 152018 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.00593

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0789 AC: 12003 AN: 152136 Hom.: 1138 Cov.: 32 AF XY: 0.0798 AC XY: 5939 AN XY: 74384

African (AFR) AF: 0.223 AC: 9271 AN: 41500

American (AMR) AF: 0.0408 AC: 623 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3468

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.115 AC: 556 AN: 4822

European-Finnish (FIN) AF: 0.00593 AC: 63 AN: 10616

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0160 AC: 1090 AN: 67960

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0343 Hom.: 460

Bravo AF: 0.0859

Asia WGS AF: 0.0620 AC: 216 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	2.7
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17055893; hg19: chr13-38063628;