3-61141532-T-C

Position:

• chr3-61141532-T-C

Variant summary

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

The NM_002012.4(FHIT):​c.-164+59085A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 145,882 control chromosomes in the GnomAD database, including 5,812 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 0.26 (5812 hom., cov: 31)
• Consequence: FHIT NM_002012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FHIT	NM_002012.4	c.-164+59085A>G		intron_variant		ENST00000492590.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FHIT	ENST00000492590.6	c.-164+59085A>G		intron_variant		1	NM_002012.4	P1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 38212 AN: 145752 Hom.: 5818 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.262 AC: 38233 AN: 145882 Hom.: 5812 Cov.: 31 AF XY: 0.267 AC XY: 19068 AN XY: 71358

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.221

Alfa AF: 0.236 Hom.: 6808

Bravo AF: 0.255

Asia WGS AF: 0.324 AC: 1125 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.57

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: rs9877396; hg19: chr3-61127205;