rs10510007

Variant names:

• chr10-114876962-A-G
• rs10510007
• ENST00000369250.7:c.2192+15628A>G

Variant summary

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

The ENST00000369250.7(FHIP2A):​c.2192+15628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,012 control chromosomes in the GnomAD database, including 8,744 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 0.33 (8744 hom., cov: 32)
• Consequence: FHIP2A ENST00000369250.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 7 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHIP2A	NM_001135051.2	c.2192+15628A>G		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	c.2192+15628A>G		intron_variant	Intron 16 of 16	1		ENSP00000358253.3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50255 AN: 150892 Hom.: 8741 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.333 AC: 50274 AN: 151012 Hom.: 8744 Cov.: 32 AF XY: 0.327 AC XY: 24171 AN XY: 73828

African (AFR) AF: 0.278 AC: 11316 AN: 40648

American (AMR) AF: 0.267 AC: 4049 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3468

East Asian (EAS) AF: 0.107 AC: 550 AN: 5140

South Asian (SAS) AF: 0.376 AC: 1807 AN: 4808

European-Finnish (FIN) AF: 0.319 AC: 3352 AN: 10520

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26695 AN: 67964

Other (OTH) AF: 0.346 AC: 727 AN: 2102

Alfa AF: 0.367 Hom.: 19243

Bravo AF: 0.319

Asia WGS AF: 0.270 AC: 940 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	7.2
DANN	Benign	0.68
PhyloP100		1.1
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: rs10510007; hg19: chr10-116636721;