Genetic Variant ENSG00000293310:n.1129A>C (chr10-122898041-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 ENST00000425266.4(ENSG00000293310):n.1129A>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 0.0262 in 224,204 control chromosomes in the GnomAD database, including 113 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 0.028 ( 87 hom., cov: 32)

Exomes 𝑓: 0.022 ( 26 hom. )

Consequence

ENSG00000293310
ENST00000425266.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

4 publications found

Variant links:

Genes affected

ENSG00000293310 (HGNC:):

ENSG00000293310 links:

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

C10orf88B 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf88B	NR_027282.1 link	n.1439A>C		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293310	ENST00000425266.4 link	n.1129A>C	non_coding_transcript_exon_variant	Exon 6 of 6	2
ENSG00000293310	ENST00000750902.1 link	n.1228A>C	non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000293310	ENST00000750903.1 link	n.954A>C	non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0284

AC:

4319

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0462

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0220

Gnomad ASJ

AF:

0.0481

Gnomad EAS

AF:

0.0819

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.00971

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0148

GnomAD4 exome

AF:

0.0216

AC:

1553

AN:

71984

Hom.:

Cov.:

AF XY:

0.0199

AC XY:

819

AN XY:

41112

show subpopulations

African (AFR)

AF:

0.0500

AC:

AN:

1600

American (AMR)

AF:

0.0421

AC:

309

AN:

7332

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

1018

East Asian (EAS)

AF:

0.0902

AC:

349

AN:

3868

South Asian (SAS)

AF:

0.0159

AC:

102

AN:

6402

European-Finnish (FIN)

AF:

0.00945

AC:

177

AN:

18736

Middle Eastern (MID)

AF:

0.0106

AC:

AN:

848

European-Non Finnish (NFE)

AF:

0.0152

AC:

452

AN:

29720

Other (OTH)

AF:

0.0195

AC:

AN:

2460

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

149

224

298

373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.0284

AC:

4329

AN:

152220

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

2161

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0462

AC:

1920

AN:

41548

American (AMR)

AF:

0.0220

AC:

337

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0481

AC:

167

AN:

3470

East Asian (EAS)

AF:

0.0821

AC:

425

AN:

5178

South Asian (SAS)

AF:

0.0149

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00971

AC:

103

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0181

AC:

1233

AN:

67980

Other (OTH)

AF:

0.0161

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

216

431

647

862

1078

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0262

Hom.:

Bravo

AF:

0.0312

Asia WGS

AF:

0.0430

AC:

148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.13

(source)

DANN

Benign

0.79

PhyloP100

-2.0

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