chr5-170109146-A-G

Position:

• chr5-170109146-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012188.5(FOXI1):​c.*535A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 153,512 control chromosomes in the GnomAD database, including 51,778 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.82 (51310 hom., cov: 31)
  • Exomes 𝑓: 0.79 (468 hom.)
• Consequence: FOXI1 NM_012188.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.05

Genes affected

FOXI1 (HGNC:3815): (forkhead box I1) This gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. This gene may play an important role in the development of the cochlea and vestibulum, as well as in embryogenesis. The encoded protein has been found to be required for the transcription of four subunits of a proton pump found in the inner ear, the kidney, and the epididymis. Mutations in this gene have been associated with deafness, autosomal recessive 4. [provided by RefSeq, Jan 2017]

FOXI1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 5-170109146-A-G is Benign according to our data. Variant chr5-170109146-A-G is described in ClinVar as [Benign]. Clinvar id is 352719.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXI1	NM_012188.5	c.*535A>G		3_prime_UTR_variant	2/2	ENST00000306268.8	NP_036320.2
FOXI1	NM_144769.4	c.*535A>G		3_prime_UTR_variant	2/2		NP_658982.1
FOXI1	XR_941092.2	n.1878A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXI1	ENST00000306268.8	c.*535A>G		3_prime_UTR_variant	2/2	1	NM_012188.5	ENSP00000304286.5
FOXI1	ENST00000449804.4	c.*535A>G		3_prime_UTR_variant	2/2	1		ENSP00000415483.2

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124646 AN: 151940 Hom.: 51267 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.794 AC: 1154 AN: 1454 Hom.: 468 Cov.: 0 AF XY: 0.805 AC XY: 605 AN XY: 752

Gnomad4 AFR exome AF: 0.929

Gnomad4 AMR exome AF: 0.839

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.922

Gnomad4 FIN exome AF: 0.737

Gnomad4 NFE exome AF: 0.776

Gnomad4 OTH exome AF: 0.714

GnomAD4 genome AF: 0.820 AC: 124744 AN: 152058 Hom.: 51310 Cov.: 31 AF XY: 0.820 AC XY: 60928 AN XY: 74308

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.830

Alfa AF: 0.813 Hom.: 51936

Bravo AF: 0.829

Asia WGS AF: 0.902 AC: 3137 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.64

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: rs6555888; hg19: chr5-169536150;