rs11665896

Variant names:

• chr19-48758426-G-A
• rs11665896
• NM_019113.4:c.*206G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-48758426-G-A
• chr19-48758426-G-C
• chr19-48758426-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_019113.4(FGF21):​c.*206G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000044 in 454,344 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: FGF21 NM_019113.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 7 publications found

Genes affected

FGF21 (HGNC:3678): (fibroblast growth factor 21) Theis gene encodes 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. This protein is a secreted endocrine factor that functions as a major metabolic regulator. The encoded protein stimulates the uptake of glucose in adipose tissue. [provided by RefSeq, Mar 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF21	NM_019113.4	c.*206G>A		downstream_gene_variant		ENST00000593756.6	NP_061986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF21	ENST00000593756.6	c.*206G>A		downstream_gene_variant		1	NM_019113.4	ENSP00000471477.1
FGF21	ENST00000222157.5	c.*206G>A		downstream_gene_variant		1		ENSP00000222157.3

Frequencies

GnomAD3 genomes AF: 0.00000660 AC: 1 AN: 151616 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000330 AC: 1 AN: 302728 Hom.: 0 AF XY: 0.00000642 AC XY: 1 AN XY: 155688

African (AFR) AF: 0.00 AC: 0 AN: 7568

American (AMR) AF: 0.00 AC: 0 AN: 9864

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10078

East Asian (EAS) AF: 0.00 AC: 0 AN: 23058

South Asian (SAS) AF: 0.00 AC: 0 AN: 13260

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23412

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1446

European-Non Finnish (NFE) AF: 0.00000512 AC: 1 AN: 195394

Other (OTH) AF: 0.00 AC: 0 AN: 18648

GnomAD4 genome AF: 0.00000660 AC: 1 AN: 151616 Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1 AN XY: 74046

African (AFR) AF: 0.0000243 AC: 1 AN: 41212

American (AMR) AF: 0.00 AC: 0 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5132

South Asian (SAS) AF: 0.00 AC: 0 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10488

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67964

Other (OTH) AF: 0.00 AC: 0 AN: 2084

Alfa AF: 0.00 Hom.: 10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.96
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11665896; hg19: chr19-49261683;