rs7099208

Variant names:

• chr10-114894815-A-G
• rs7099208
• ENST00000369250.7:c.2193-4675A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135051.2(FHIP2A):​c.2193-4675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,088 control chromosomes in the GnomAD database, including 10,257 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 0.36 (10257 hom., cov: 32)
• Consequence: FHIP2A NM_001135051.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 13 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135051.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHIP2A	NM_001135051.2		c.2193-4675A>G		intron	N/A	NP_001128523.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHIP2A	ENST00000369250.7	TSL:1	c.2193-4675A>G		intron	N/A	ENSP00000358253.3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54684 AN: 151970 Hom.: 10243 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.360 AC: 54748 AN: 152088 Hom.: 10257 Cov.: 32 AF XY: 0.358 AC XY: 26620 AN XY: 74356

African (AFR) AF: 0.284 AC: 11775 AN: 41492

American (AMR) AF: 0.393 AC: 6010 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3468

East Asian (EAS) AF: 0.0748 AC: 388 AN: 5186

South Asian (SAS) AF: 0.352 AC: 1698 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4050 AN: 10564

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28106 AN: 67962

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.391 Hom.: 19810

Bravo AF: 0.355

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.70
PhyloP100		0.082
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7099208; hg19: chr10-116654574;