chr17-7442983-T-C

Variant names:

• chr17-7442983-T-C
• rs3853818
• ENST00000575331.1:n.2570T>C

Variant summary

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

The ENST00000575331.1(ENSG00000272884):​n.2570T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,172,598 control chromosomes in the GnomAD database, including 166,920 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 0.46 (17568 hom., cov: 31)
  • Exomes 𝑓: 0.52 (149352 hom.)
• Consequence: ENSG00000272884 ENST00000575331.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 19 publications found

Genes affected

ENSG00000272884 (HGNC:):

FGF11 (HGNC:3667): (fibroblast growth factor 11) 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. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

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 = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF11	NM_004112.4	c.608-93T>C		intron_variant	Intron 4 of 4	ENST00000293829.9	NP_004103.1
FGF11	NM_001303460.2	c.431-93T>C		intron_variant	Intron 4 of 4		NP_001290389.1
FGF11	NR_130156.2	n.648-93T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF11	ENST00000293829.9	c.608-93T>C		intron_variant	Intron 4 of 4	1	NM_004112.4	ENSP00000293829.4

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70173 AN: 151834 Hom.: 17571 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.523 AC: 533550 AN: 1020646 Hom.: 149352 Cov.: 13 AF XY: 0.520 AC XY: 270786 AN XY: 520334

African (AFR) AF: 0.343 AC: 8422 AN: 24554

American (AMR) AF: 0.293 AC: 11164 AN: 38080

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 11805 AN: 20214

East Asian (EAS) AF: 0.0384 AC: 1446 AN: 37618

South Asian (SAS) AF: 0.385 AC: 27015 AN: 70162

European-Finnish (FIN) AF: 0.457 AC: 22967 AN: 50252

Middle Eastern (MID) AF: 0.604 AC: 2868 AN: 4752

European-Non Finnish (NFE) AF: 0.582 AC: 424805 AN: 729512

Other (OTH) AF: 0.507 AC: 23058 AN: 45502

GnomAD4 genome AF: 0.462 AC: 70180 AN: 151952 Hom.: 17568 Cov.: 31 AF XY: 0.451 AC XY: 33489 AN XY: 74276

African (AFR) AF: 0.353 AC: 14628 AN: 41418

American (AMR) AF: 0.394 AC: 6021 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3468

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5182

South Asian (SAS) AF: 0.385 AC: 1857 AN: 4818

European-Finnish (FIN) AF: 0.443 AC: 4671 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38966 AN: 67924

Other (OTH) AF: 0.503 AC: 1063 AN: 2114

Alfa AF: 0.552 Hom.: 38739

Bravo AF: 0.454

Asia WGS AF: 0.196 AC: 683 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	4.5
DANN	Benign	0.58
PhyloP100		0.10
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: rs3853818; hg19: chr17-7346302; COSMIC: COSV53439221; COSMIC: COSV53439221;