chr1-93519247-G-C

Variant names:

• chr1-93519247-G-C
• rs4847431
• NM_001164473.3:c.141-2835G>C

Variant summary

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

The NM_001164473.3(FNBP1L):​c.141-2835G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,948 control chromosomes in the GnomAD database, including 21,615 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 0.51 (21615 hom., cov: 31)
• Consequence: FNBP1L NM_001164473.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 4 publications found

Genes affected

FNBP1L (HGNC:20851): (formin binding protein 1 like) The protein encoded by this gene binds to both CDC42 and N-WASP. This protein promotes CDC42-induced actin polymerization by activating the N-WASP-WIP complex and, therefore, is involved in a pathway that links cell surface signals to the actin cytoskeleton. Alternative splicing results in multiple transcript variants encoding different isoforms. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNBP1L	NM_001164473.3	c.141-2835G>C		intron_variant	Intron 2 of 16	ENST00000271234.13	NP_001157945.1
FNBP1L	NM_001024948.3	c.141-2835G>C		intron_variant	Intron 2 of 13		NP_001020119.1
FNBP1L	NM_017737.5	c.141-2835G>C		intron_variant	Intron 2 of 14		NP_060207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNBP1L	ENST00000271234.13	c.141-2835G>C		intron_variant	Intron 2 of 16	5	NM_001164473.3	ENSP00000271234.7
FNBP1L	ENST00000260506.12	c.141-2835G>C		intron_variant	Intron 2 of 13	1		ENSP00000260506.8
FNBP1L	ENST00000370253.6	c.141-2835G>C		intron_variant	Intron 2 of 14	5		ENSP00000359275.2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76931 AN: 151830 Hom.: 21603 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.506 AC: 76959 AN: 151948 Hom.: 21615 Cov.: 31 AF XY: 0.509 AC XY: 37790 AN XY: 74292

African (AFR) AF: 0.249 AC: 10300 AN: 41406

American (AMR) AF: 0.518 AC: 7905 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2224 AN: 3464

East Asian (EAS) AF: 0.632 AC: 3263 AN: 5160

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6821 AN: 10574

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41816 AN: 67938

Other (OTH) AF: 0.543 AC: 1147 AN: 2114

Alfa AF: 0.429 Hom.: 1342

Bravo AF: 0.481

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		0.049
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: rs4847431; hg19: chr1-93984804;