dbSNP rs17286683: ANKHD1-DT:n.154T>G (chr5-140401510-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000507521.3(ANKHD1-DT):n.154T>G 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 0.182 in 158,782 control chromosomes in the GnomAD database, including 3,408 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 0.18 ( 3236 hom., cov: 32)

Exomes 𝑓: 0.21 ( 172 hom. )

Consequence

ANKHD1-DT
ENST00000507521.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0480

Publications

5 publications found

Variant links:

Genes affected

ANKHD1-DT (HGNC:55564): (ANKHD1 divergent transcript)

ANKHD1-DT links:

ENSG00000302458 (HGNC:):

ENSG00000302458 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=-0.61).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
ANKHD1-DT	NR_186044.1 link	n.-109T>G	upstream_gene_variant
ANKHD1-DT	NR_186045.1 link	n.-109T>G	upstream_gene_variant
ANKHD1-DT	NR_186046.1 link	n.-109T>G	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ANKHD1-DT	ENST00000507521.3 link	n.154T>G	non_coding_transcript_exon_variant	Exon 1 of 2	2
ANKHD1-DT	ENST00000687631.3 link	n.183T>G	non_coding_transcript_exon_variant	Exon 1 of 1
ANKHD1-DT	ENST00000786872.1 link	n.197T>G	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27549

AN:

152140

Hom.:

3227

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0441

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.215

AC:

1401

AN:

6524

Hom.:

172

AF XY:

0.223

AC XY:

794

AN XY:

3568

show subpopulations

African (AFR)

AF:

0.0714

AC:

AN:

238

American (AMR)

AF:

0.183

AC:

AN:

180

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

AN:

270

East Asian (EAS)

AF:

0.292

AC:

AN:

178

South Asian (SAS)

AF:

0.239

AC:

200

AN:

836

European-Finnish (FIN)

AF:

0.285

AC:

AN:

200

Middle Eastern (MID)

AF:

0.125

AC:

AN:

European-Non Finnish (NFE)

AF:

0.216

AC:

913

AN:

4224

Other (OTH)

AF:

0.178

AC:

AN:

382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

114

171

228

285

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.181

AC:

27565

AN:

152258

Hom.:

3236

Cov.:

AF XY:

0.184

AC XY:

13674

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0439

AC:

1826

AN:

41576

American (AMR)

AF:

0.211

AC:

3231

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

685

AN:

3472

East Asian (EAS)

AF:

0.290

AC:

1500

AN:

5176

South Asian (SAS)

AF:

0.266

AC:

1284

AN:

4830

European-Finnish (FIN)

AF:

0.267

AC:

2825

AN:

10594

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15720

AN:

68008

Other (OTH)

AF:

0.187

AC:

396

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1112

2225

3337

4450

5562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.177

Hom.:

1156

Bravo

AF:

0.169

Asia WGS

AF:

0.284

AC:

989

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

-0.048

PromoterAI

-0.018

Neutral

(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