rs7490

Positions:

• chr8-22104323-G-A
• chr8-22104323-G-C
• chr8-22104323-G-T

Variant summary

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

The NM_022749.7(FHIP2B):​c.*1392G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,254 control chromosomes in the GnomAD database, including 15,756 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 0.44 (15704 hom., cov: 32)
  • Exomes 𝑓: 0.56 (52 hom.)
• Consequence: FHIP2B NM_022749.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

FHIP2B (HGNC:16492): (FHF complex subunit HOOK interacting protein 2B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FHIP2B	NM_022749.7	c.*1392G>A		3_prime_UTR_variant	17/17	ENST00000289921.8	NP_073586.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FHIP2B	ENST00000289921.8	c.*1392G>A		3_prime_UTR_variant	17/17	5	NM_022749.7	ENSP00000289921	P1
FHIP2B	ENST00000450006.7	c.*509G>A		3_prime_UTR_variant, NMD_transcript_variant	18/18	1		ENSP00000403288
FHIP2B	ENST00000496599.3	n.2288G>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67431 AN: 151824 Hom.: 15691 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.429

GnomAD4 exome AF: 0.564 AC: 176 AN: 312 Hom.: 52 Cov.: 0 AF XY: 0.574 AC XY: 101 AN XY: 176

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.444 AC: 67461 AN: 151942 Hom.: 15704 Cov.: 32 AF XY: 0.454 AC XY: 33737 AN XY: 74278

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.431

Alfa AF: 0.447 Hom.: 14417

Bravo AF: 0.440

Asia WGS AF: 0.563 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.0
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7490; hg19: chr8-21961834;