rs7075888

chr10-114867358-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FHIP2A	NM_001135051.2	c.2192+6024C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FHIP2A	ENST00000369250.7	c.2192+6024C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48404 AN: 151844 Hom.: 8297 Cov.: 31

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.: 31 AF XY: 0.314 AC XY: 23326 AN XY: 74278

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.333

Alfa AF: 0.345 Hom.: 1163

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
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7075888; hg19: chr10-116627117;