8-22104323-G-C

Variant names:

• chr8-22104323-G-C
• rs7490
• NM_022749.7:c.*1392G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022749.7(FHIP2B):​c.*1392G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FHIP2B NM_022749.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022749.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHIP2B	NM_022749.7	MANE Select	c.*1392G>C		3_prime_UTR	Exon 17 of 17	NP_073586.5
	FHIP2B	NM_001354250.2		c.*1392G>C		3_prime_UTR	Exon 17 of 17	NP_001341179.1
	FHIP2B	NM_001354251.2		c.*1392G>C		3_prime_UTR	Exon 18 of 18	NP_001341180.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHIP2B	ENST00000289921.8	TSL:5 MANE Select	c.*1392G>C		3_prime_UTR	Exon 17 of 17	ENSP00000289921.6	Q86V87
	FHIP2B	ENST00000450006.7	TSL:1	n.*509G>C		non_coding_transcript_exon	Exon 18 of 18	ENSP00000403288.3	Q86V87
	FHIP2B	ENST00000450006.7	TSL:1	n.*509G>C		3_prime_UTR	Exon 18 of 18	ENSP00000403288.3	Q86V87

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.62
PhyloP100		1.2

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

Other links and lift over

dbSNP: rs7490; hg19: chr8-21961834;