7-127596949-G-A

Position:

• chr7-127596949-G-A

Variant summary

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

The NM_020369.3(FSCN3):​c.960+503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,158 control chromosomes in the GnomAD database, including 3,809 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 0.19 (3809 hom., cov: 33)
• Consequence: FSCN3 NM_020369.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

FSCN3 (HGNC:3961): (fascin actin-bundling protein 3) Predicted to enable actin filament binding activity. Predicted to be involved in actin filament bundle assembly; cell migration; and establishment or maintenance of cell polarity. Predicted to be located in cytoskeleton. Predicted to be active in several cellular components, including lamellipodium; microvillus; and ruffle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSCN3	NM_020369.3	c.960+503G>A		intron_variant		ENST00000265825.6	NP_065102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSCN3	ENST00000265825.6	c.960+503G>A		intron_variant		1	NM_020369.3	ENSP00000265825	P1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28991 AN: 152042 Hom.: 3805 Cov.: 33

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.191 AC: 29011 AN: 152158 Hom.: 3809 Cov.: 33 AF XY: 0.199 AC XY: 14781 AN XY: 74376

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.197

Alfa AF: 0.205 Hom.: 1772

Bravo AF: 0.181

Asia WGS AF: 0.403 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.47

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: rs806214; hg19: chr7-127237003;