rs6501841

Variant names:

• chr17-75928005-G-A
• rs6501841
• NM_001319193.2:c.397+71C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-75928005-G-A
• chr17-75928005-G-C

Variant summary

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

The NM_001319193.2(FBF1):​c.397+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00727 in 1,273,112 control chromosomes in the GnomAD database, including 280 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 0.026 (150 hom., cov: 32)
  • Exomes 𝑓: 0.0047 (130 hom.)
• Consequence: FBF1 NM_001319193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

Genes affected

FBF1 (HGNC:24674): (Fas binding factor 1) Involved in apical junction assembly and establishment of epithelial cell polarity. Acts upstream of or within cilium assembly. Located in centriole; centrosome; and spindle pole. Part of ciliary transition fiber. Colocalizes with apical junction complex and keratin filament. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBF1	NM_001319193.2	c.397+71C>T		intron_variant	Intron 8 of 29	ENST00000636174.2	NP_001306122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBF1	ENST00000636174.2	c.397+71C>T		intron_variant	Intron 8 of 29	5	NM_001319193.2	ENSP00000490726.1

Frequencies

GnomAD3 genomes AF: 0.0258 AC: 3926 AN: 152106 Hom.: 150 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000720

Gnomad OTH AF: 0.0225

GnomAD4 exome AF: 0.00474 AC: 5316 AN: 1120888 Hom.: 130 AF XY: 0.00465 AC XY: 2647 AN XY: 568926

African (AFR) AF: 0.0766 AC: 1967 AN: 25670

American (AMR) AF: 0.0295 AC: 1003 AN: 34032

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22538

East Asian (EAS) AF: 0.0182 AC: 688 AN: 37776

South Asian (SAS) AF: 0.0113 AC: 858 AN: 76146

European-Finnish (FIN) AF: 0.000937 AC: 49 AN: 52312

Middle Eastern (MID) AF: 0.00852 AC: 30 AN: 3522

European-Non Finnish (NFE) AF: 0.000313 AC: 257 AN: 820308

Other (OTH) AF: 0.00955 AC: 464 AN: 48584

GnomAD4 genome AF: 0.0258 AC: 3934 AN: 152224 Hom.: 150 Cov.: 32 AF XY: 0.0255 AC XY: 1899 AN XY: 74412

African (AFR) AF: 0.0793 AC: 3293 AN: 41524

American (AMR) AF: 0.0215 AC: 328 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5180

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4828

European-Finnish (FIN) AF: 0.000566 AC: 6 AN: 10594

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000720 AC: 49 AN: 68022

Other (OTH) AF: 0.0227 AC: 48 AN: 2112

Alfa AF: 0.0210 Hom.: 16

Bravo AF: 0.0305

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.57
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6501841; hg19: chr17-73924086;