Genetic Variant FHIP2A:c.2192+6024C>T (chr10-114867358-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 ENST00000369250.7(FHIP2A):c.2192+6024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,962 control chromosomes in the GnomAD database, including 8,304 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 0.32 ( 8304 hom., cov: 31)

Consequence

FHIP2A
ENST00000369250.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

2 publications found

Variant links:

Genes affected

FHIP2A (HGNC:29320): (FHF complex subunit HOOK interacting protein 2A)

FHIP2A 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHIP2A	NM_001135051.2 link	c.2192+6024C>T		intron_variant	Intron 16 of 16		NP_001128523.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FHIP2A	ENST00000369250.7 link	c.2192+6024C>T		intron_variant	Intron 16 of 16	1		ENSP00000358253.3		Q5W0V3-2

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48404

AN:

151844

Hom.:

8297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.410

Gnomad EAS

AF:

0.0364

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.316

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.329

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

GnomAD4 genome

AF:

0.319

AC:

48433

AN:

151962

Hom.:

8304

Cov.:

AF XY:

0.314

AC XY:

23326

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.254

AC:

10520

AN:

41412

American (AMR)

AF:

0.254

AC:

3878

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.410

AC:

1423

AN:

3472

East Asian (EAS)

AF:

0.0365

AC:

189

AN:

5174

South Asian (SAS)

AF:

0.368

AC:

1772

AN:

4816

European-Finnish (FIN)

AF:

0.316

AC:

3331

AN:

10548

Middle Eastern (MID)

AF:

0.353

AC:

103

AN:

292

European-Non Finnish (NFE)

AF:

0.386

AC:

26245

AN:

67952

Other (OTH)

AF:

0.333

AC:

703

AN:

2110

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

Alfa

AF:

0.342

Hom.:

1188

Bravo

AF:

0.306

Asia WGS

AF:

0.247

AC:

863

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.4

(source)

DANN

Benign

0.72

PhyloP100

0.16

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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chr10-114867358-C-T

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