rs445057

Positions:

• chr3-60461636-C-T

Variant summary

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

The NM_002012.4(FHIT):​c.103+75224G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,044 control chromosomes in the GnomAD database, including 9,803 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 0.31 (9803 hom., cov: 32)
• Consequence: FHIT NM_002012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

FHIT (HGNC:3701): (fragile histidine triad diadenosine triphosphatase) The protein encoded by this gene is a P1-P3-bis(5'-adenosyl) triphosphate hydrolase involved in purine metabolism. This gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas. The encoded protein is also a tumor suppressor, as loss of its activity results in replication stress and DNA damage. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FHIT	NM_002012.4	c.103+75224G>A		intron_variant		ENST00000492590.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FHIT	ENST00000492590.6	c.103+75224G>A		intron_variant		1	NM_002012.4	P1
FHIT	ENST00000476844.5	c.103+75224G>A		intron_variant		1		P1
FHIT	ENST00000468189.5	c.103+75224G>A		intron_variant		2		P1
FHIT	ENST00000488467.5	c.103+75224G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46909 AN: 151926 Hom.: 9779 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 46981 AN: 152044 Hom.: 9803 Cov.: 32 AF XY: 0.308 AC XY: 22876 AN XY: 74312

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.300

Alfa AF: 0.202 Hom.: 4812

Bravo AF: 0.331

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.44

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: rs445057; hg19: chr3-60447369;