dbSNP rs1216119: ENSG00000260599:n.907G>T (chr19-22527043-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000562262.1(ENSG00000260599):n.907G>T 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 0.297 in 152,078 control chromosomes in the GnomAD database, including 7,270 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 0.30 ( 7268 hom., cov: 32)

Exomes 𝑓: 0.35 ( 2 hom. )

Consequence

ENSG00000260599
ENST00000562262.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Publications

7 publications found

Variant links:

Genes affected

ENSG00000260599 (HGNC:):

ENSG00000260599 links:

ZNF98 (HGNC:13174): (zinc finger protein 98) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF98 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101929124	NR_110427.1 link	n.907G>T	non_coding_transcript_exon_variant	Exon 1 of 5
LOC105376917	NR_160727.1 link	n.147+5296G>T	intron_variant	Intron 1 of 2
LOC105376917	NR_160728.1 link	n.147+5296G>T	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000260599	ENST00000562262.1 link	n.907G>T	non_coding_transcript_exon_variant	Exon 1 of 5	2
ZNF98	ENST00000593802.1 link	c.48+5296G>T	intron_variant	Intron 1 of 2	3	ENSP00000472301.1	M0R243
ZNF98	ENST00000599879.1 link	n.147+5296G>T	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45054

AN:

151920

Hom.:

7261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.350

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.375

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.321

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.297

AC:

45100

AN:

152038

Hom.:

7268

Cov.:

AF XY:

0.305

AC XY:

22630

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.251

AC:

10416

AN:

41492

American (AMR)

AF:

0.350

AC:

5339

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

895

AN:

3470

East Asian (EAS)

AF:

0.577

AC:

2950

AN:

5112

South Asian (SAS)

AF:

0.524

AC:

2527

AN:

4822

European-Finnish (FIN)

AF:

0.343

AC:

3620

AN:

10562

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18511

AN:

67984

Other (OTH)

AF:

0.307

AC:

650

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1623

3246

4868

6491

8114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.298

Hom.:

6376

Bravo

AF:

0.297

Asia WGS

AF:

0.551

AC:

1911

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

6.5

(source)

DANN

Benign

0.33

PhyloP100

0.12

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