chr15-49487038-T-A

Variant names:

• chr15-49487038-T-A
• rs11630629
• NM_002009.4:c.*2534T>A

Variant summary

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

The NM_002009.4(FGF7):​c.*2534T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,778 control chromosomes in the GnomAD database, including 6,017 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 0.28 (6017 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: FGF7 NM_002009.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

Genes affected

FGF7 (HGNC:3685): (fibroblast growth factor 7) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein is a potent epithelial cell-specific growth factor, whose mitogenic activity is predominantly exhibited in keratinocytes but not in fibroblasts and endothelial cells. Studies of mouse and rat homologs of this gene implicated roles in morphogenesis of epithelium, reepithelialization of wounds, hair development and early lung organogenesis. [provided by RefSeq, Jul 2008]

FAM227B (HGNC:26543): (family with sequence similarity 227 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF7	NM_002009.4	c.*2534T>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000267843.9	NP_002000.1
FAM227B	NM_152647.3	c.1012+21173A>T		intron_variant	Intron 11 of 15	ENST00000299338.11	NP_689860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF7	ENST00000267843.9	c.*2534T>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_002009.4	ENSP00000267843.4
FAM227B	ENST00000299338.11	c.1012+21173A>T		intron_variant	Intron 11 of 15	2	NM_152647.3	ENSP00000299338.6
FAM227B	ENST00000561064.5	c.910+21173A>T		intron_variant	Intron 10 of 10	1		ENSP00000453028.1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41869 AN: 151660 Hom.: 6009 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.298

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.276 AC: 41911 AN: 151778 Hom.: 6017 Cov.: 32 AF XY: 0.277 AC XY: 20554 AN XY: 74222

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.300

Alfa AF: 0.254 Hom.: 619

Bravo AF: 0.288

Asia WGS AF: 0.319 AC: 1109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.55

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: rs11630629; hg19: chr15-49779235;