rs11630629

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-49487038-T-A
• chr15-49487038-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002009.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF7	NM_002009.4	MANE Select	c.*2534T>A		3_prime_UTR	Exon 4 of 4	NP_002000.1	P21781-1
	FAM227B	NM_152647.3	MANE Select	c.1012+21173A>T		intron	N/A	NP_689860.2	Q96M60-1
	FAM227B	NM_001330293.2		c.910+21173A>T		intron	N/A	NP_001317222.1	Q96M60-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF7	ENST00000267843.9	TSL:1 MANE Select	c.*2534T>A		3_prime_UTR	Exon 4 of 4	ENSP00000267843.4	P21781-1
	FAM227B	ENST00000299338.11	TSL:2 MANE Select	c.1012+21173A>T		intron	N/A	ENSP00000299338.6	Q96M60-1
	FAM227B	ENST00000561064.5	TSL:1	c.910+21173A>T		intron	N/A	ENSP00000453028.1	Q96M60-2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.282 AC: 11693 AN: 41432

American (AMR) AF: 0.361 AC: 5493 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3462

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5150

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4814

European-Finnish (FIN) AF: 0.244 AC: 2580 AN: 10590

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17194 AN: 67822

Other (OTH) AF: 0.300 AC: 631 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.55
PhyloP100		0.38
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: rs11630629; hg19: chr15-49779235;