rs1041211

Variant names:

• chr13-40366522-C-A
• rs1041211
• ENST00000636621.1:n.71-16220G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-40366522-C-A
• chr13-40366522-C-T

Variant summary

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

The ENST00000636621.1(LINC00598):​n.71-16220G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,204 control chromosomes in the GnomAD database, including 952 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 0.10 (952 hom., cov: 32)
• Consequence: LINC00598 ENST00000636621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 1 publications found

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636621.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	NR_024506.2		n.662-16220G>T		intron	N/A
	LINC00598	NR_024507.3		n.802-16220G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000636621.1	TSL:1	n.71-16220G>T		intron	N/A
	LINC00598	ENST00000400432.4	TSL:5	n.117-16220G>T		intron	N/A
	LINC00598	ENST00000636192.2	TSL:5	n.178-16220G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15506 AN: 152086 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.102 AC: 15544 AN: 152204 Hom.: 952 Cov.: 32 AF XY: 0.104 AC XY: 7771 AN XY: 74420

African (AFR) AF: 0.133 AC: 5527 AN: 41522

American (AMR) AF: 0.158 AC: 2424 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5174

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4828

European-Finnish (FIN) AF: 0.0781 AC: 828 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4791 AN: 68002

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

Alfa AF: 0.0795 Hom.: 915

Bravo AF: 0.115

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.47
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1041211;

hg19: chr13-40940659;