1-31374572-G-T

Position:

• chr1-31374572-G-T

Variant summary

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

The XR_007065573.1(LOC124903892):​n.89+185G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,194 control chromosomes in the GnomAD database, including 4,527 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 0.22 (4527 hom., cov: 32)
• Consequence: LOC124903892 XR_007065573.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

LOC124903892 (HGNC:):

FABP3 (HGNC:3557): (fatty acid binding protein 3) The intracellular fatty acid-binding proteins (FABPs) belongs to a multigene family. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Fatty acid-binding protein 3 gene contains four exons and its function is to arrest growth of mammary epithelial cells. This gene is a candidate tumor suppressor gene for human breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

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 = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903892	XR_007065573.1	n.89+185G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP3	ENST00000482018.1	c.-27-1531C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34154 AN: 152076 Hom.: 4521 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.225 AC: 34172 AN: 152194 Hom.: 4527 Cov.: 32 AF XY: 0.230 AC XY: 17125 AN XY: 74390

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.242

Alfa AF: 0.230 Hom.: 3989

Bravo AF: 0.221

Asia WGS AF: 0.372 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12401792; hg19: chr1-31847419; COSMIC: COSV65500285;