rs11084582

Variant names:

• chr19-31375850-C-A
• rs11084582
• ENST00000585336.1:n.251+15269C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-31375850-C-A
• chr19-31375850-C-G

Variant summary

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

The ENST00000585336.1(TSHZ3-AS1):​n.251+15269C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,030 control chromosomes in the GnomAD database, including 13,632 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 0.42 (13632 hom., cov: 33)
• Consequence: TSHZ3-AS1 ENST00000585336.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 4 publications found

Genes affected

TSHZ3-AS1 (HGNC:55288): (TSHZ3 antisense RNA 1)

LOC124904794 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585336.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHZ3-AS1	ENST00000585336.1	TSL:4	n.251+15269C>A		intron	N/A
	TSHZ3-AS1	ENST00000716204.1		n.308+26933C>A		intron	N/A
	TSHZ3-AS1	ENST00000716205.1		n.220+26933C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63641 AN: 151912 Hom.: 13610 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.419 AC: 63704 AN: 152030 Hom.: 13632 Cov.: 33 AF XY: 0.424 AC XY: 31508 AN XY: 74296

African (AFR) AF: 0.438 AC: 18151 AN: 41472

American (AMR) AF: 0.419 AC: 6396 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3127 AN: 5176

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5301 AN: 10548

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26915 AN: 67964

Other (OTH) AF: 0.383 AC: 809 AN: 2114

Alfa AF: 0.425 Hom.: 2460

Bravo AF: 0.412

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.87
PhyloP100		-0.74

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: rs11084582;

hg19: chr19-31866756;