dbSNP rs2698501: HTR5A-AS1:n.789T>C (chr7-155068981-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000395731.5(HTR5A-AS1):n.789T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 229,730 control chromosomes in the GnomAD database, including 8,543 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 0.27 ( 5855 hom., cov: 33)

Exomes 𝑓: 0.25 ( 2688 hom. )

Consequence

HTR5A-AS1
ENST00000395731.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.86

Publications

1 publications found

Variant links:

Genes affected

HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

HTR5A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A-AS1	NR_038945.1 link	n.789T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HTR5A-AS1	ENST00000395731.5 link	n.789T>C	non_coding_transcript_exon_variant	Exon 2 of 2	1
HTR5A-AS1	ENST00000493904.3 link	n.816T>C	non_coding_transcript_exon_variant	Exon 2 of 2	4
HTR5A-AS1	ENST00000655797.2 link	n.1114T>C	non_coding_transcript_exon_variant	Exon 3 of 3
HTR5A-AS1	ENST00000671665.1 link	n.1682T>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41507

AN:

152000

Hom.:

5852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.260

GnomAD4 exome

AF:

0.245

AC:

19037

AN:

77612

Hom.:

2688

Cov.:

AF XY:

0.245

AC XY:

10382

AN XY:

42404

show subpopulations

African (AFR)

AF:

0.242

AC:

292

AN:

1206

American (AMR)

AF:

0.191

AC:

405

AN:

2116

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

339

AN:

1642

East Asian (EAS)

AF:

0.396

AC:

713

AN:

1800

South Asian (SAS)

AF:

0.226

AC:

3251

AN:

14394

European-Finnish (FIN)

AF:

0.237

AC:

1353

AN:

5710

Middle Eastern (MID)

AF:

0.241

AC:

179

AN:

742

European-Non Finnish (NFE)

AF:

0.251

AC:

11538

AN:

46002

Other (OTH)

AF:

0.242

AC:

967

AN:

4000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

677

1353

2030

2706

3383

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.273

AC:

41524

AN:

152118

Hom.:

5855

Cov.:

AF XY:

0.272

AC XY:

20260

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.269

AC:

11160

AN:

41494

American (AMR)

AF:

0.227

AC:

3470

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

800

AN:

3468

East Asian (EAS)

AF:

0.424

AC:

2192

AN:

5168

South Asian (SAS)

AF:

0.259

AC:

1250

AN:

4824

European-Finnish (FIN)

AF:

0.268

AC:

2828

AN:

10570

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.277

AC:

18865

AN:

67990

Other (OTH)

AF:

0.259

AC:

547

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1589

3177

4766

6354

7943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.268

Hom.:

1210

Bravo

AF:

0.271

Asia WGS

AF:

0.306

AC:

1064

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.3

(source)

DANN

Benign

0.72

PhyloP100

1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over