rs7490

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000450006.7(FHIP2B):​n.*509G>A variant causes a non coding transcript exon 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 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
FHIP2B	NM_022749.7	c.*1392G>A		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>A		non_coding_transcript_exon_variant	Exon 18 of 18	1		ENSP00000403288.3
FHIP2B	ENST00000289921.8	c.*1392G>A		3_prime_UTR_variant	Exon 17 of 17	5	NM_022749.7	ENSP00000289921.6
FHIP2B	ENST00000450006.7	n.*509G>A		3_prime_UTR_variant	Exon 18 of 18	1		ENSP00000403288.3
FHIP2B	ENST00000496599.3	n.2288G>A		non_coding_transcript_exon_variant	Exon 4 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.563 AC: 169 AN: 300

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 5 AN: 8

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.336 AC: 13895 AN: 41412

American (AMR) AF: 0.578 AC: 8842 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3107 AN: 5146

South Asian (SAS) AF: 0.494 AC: 2380 AN: 4820

European-Finnish (FIN) AF: 0.589 AC: 6220 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30468 AN: 67942

Other (OTH) AF: 0.431 AC: 907 AN: 2102

Alfa AF: 0.446 Hom.: 19056

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
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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;