8-22104323-G-T

Variant names:

• chr8-22104323-G-T
• rs7490
• ENST00000450006.7:n.*509G>T

Variant summary

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

The ENST00000450006.7(FHIP2B):​n.*509G>T variant causes a non coding transcript exon 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 ENST00000450006.7 non_coding_transcript_exon
• 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=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHIP2B	NM_022749.7	c.*1392G>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000289921.8	NP_073586.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FHIP2B	ENST00000450006.7	n.*509G>T		non_coding_transcript_exon_variant	Exon 18 of 18	1		ENSP00000403288.3
FHIP2B	ENST00000289921.8	c.*1392G>T		3_prime_UTR_variant	Exon 17 of 17	5	NM_022749.7	ENSP00000289921.6
FHIP2B	ENST00000450006.7	n.*509G>T		3_prime_UTR_variant	Exon 18 of 18	1		ENSP00000403288.3
FHIP2B	ENST00000496599.3	n.2288G>T		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.74
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;