15-49431258-G-C

Variant names:

• chr15-49431258-G-C
• rs11855798
• NM_152647.3:c.1013-59859C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152647.3(FAM227B):​c.1013-59859C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,604 control chromosomes in the GnomAD database, including 7,130 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 (7130 hom., cov: 32)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 2 publications found

Genes affected

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

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152647.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM227B	NM_152647.3	MANE Select	c.1013-59859C>G		intron	N/A	NP_689860.2
	FGF7	NM_002009.4	MANE Select	c.286+6675G>C		intron	N/A	NP_002000.1
	FAM227B	NM_001330293.2		c.911-8544C>G		intron	N/A	NP_001317222.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM227B	ENST00000299338.11	TSL:2 MANE Select	c.1013-59859C>G		intron	N/A	ENSP00000299338.6
	FGF7	ENST00000267843.9	TSL:1 MANE Select	c.286+6675G>C		intron	N/A	ENSP00000267843.4
	FAM227B	ENST00000561064.5	TSL:1	c.911-8544C>G		intron	N/A	ENSP00000453028.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42013 AN: 151486 Hom.: 7129 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.277 AC: 41997 AN: 151604 Hom.: 7130 Cov.: 32 AF XY: 0.275 AC XY: 20388 AN XY: 74038

African (AFR) AF: 0.0895 AC: 3707 AN: 41410

American (AMR) AF: 0.269 AC: 4085 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3466

East Asian (EAS) AF: 0.185 AC: 950 AN: 5126

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4818

European-Finnish (FIN) AF: 0.342 AC: 3602 AN: 10542

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25966 AN: 67746

Other (OTH) AF: 0.285 AC: 599 AN: 2102

Alfa AF: 0.196 Hom.: 474

Bravo AF: 0.264

Asia WGS AF: 0.179 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.53
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11855798; hg19: chr15-49723455;