Genetic Variant ENST00000557398.2:c.-90+2614G>A (chr15-92696426-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000557398.2(FAM174B):c.-90+2614G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,210 control chromosomes in the GnomAD database, including 1,787 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 0.15 ( 1787 hom., cov: 32)

Consequence

FAM174B
ENST00000557398.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

1 publications found

Variant links:

Genes affected

FAM174B (HGNC:34339): (family with sequence similarity 174 member B) Involved in Golgi organization. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM174B links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM174B	ENST00000557398.2 link	c.-90+2614G>A		intron_variant	Intron 2 of 3	4		ENSP00000456099.2		H3BR69

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22990

AN:

152090

Hom.:

1789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.0117

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.151

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

GnomAD4 genome

AF:

0.151

AC:

22977

AN:

152210

Hom.:

1787

Cov.:

AF XY:

0.150

AC XY:

11186

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.148

AC:

6134

AN:

41512

American (AMR)

AF:

0.118

AC:

1803

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

556

AN:

3472

East Asian (EAS)

AF:

0.0116

AC:

AN:

5192

South Asian (SAS)

AF:

0.220

AC:

1062

AN:

4820

European-Finnish (FIN)

AF:

0.129

AC:

1366

AN:

10596

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.170

AC:

11560

AN:

68004

Other (OTH)

AF:

0.148

AC:

314

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1021

2042

3062

4083

5104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.162

Hom.:

310

Bravo

AF:

0.147

Asia WGS

AF:

0.126

AC:

441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.4

(source)

DANN

Benign

0.77

PhyloP100

-0.031

Splicing

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

Publications

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ENST00000557398.2:c.-90+2614G>A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over