3-128925973-C-T

Variant names:

• chr3-128925973-C-T
• rs1680785
• NM_001394090.1:c.2751+6727G>A

Variant summary

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

The NM_001394090.1(CFAP92):​c.2751+6727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,976 control chromosomes in the GnomAD database, including 16,719 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 0.43 (16719 hom., cov: 32)
• Consequence: CFAP92 NM_001394090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 2 publications found

Genes affected

CFAP92 (HGNC:29231): (cilia and flagella associated protein 92 (putative))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394090.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP92	NM_001394090.1	MANE Select	c.2751+6727G>A		intron	N/A	NP_001381019.1	A0A2R8YFM9
	CFAP92	NM_001348520.2		c.1878+6727G>A		intron	N/A	NP_001335449.1
	CFAP92	NM_001348521.2		c.1782+6727G>A		intron	N/A	NP_001335450.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP92	ENST00000645291.3	MANE Select	c.2751+6727G>A		intron	N/A	ENSP00000496592.2	A0A2R8YFM9
	CFAP92	ENST00000511438.5	TSL:2	c.1169-15640G>A		intron	N/A	ENSP00000426217.1	D6RH05
	CFAP92	ENST00000669741.1		c.561+6727G>A		intron	N/A	ENSP00000499631.1	A0A590UJZ5

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65674 AN: 151858 Hom.: 16685 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.433 AC: 65759 AN: 151976 Hom.: 16719 Cov.: 32 AF XY: 0.429 AC XY: 31898 AN XY: 74302

African (AFR) AF: 0.701 AC: 29061 AN: 41428

American (AMR) AF: 0.399 AC: 6094 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3466

East Asian (EAS) AF: 0.638 AC: 3290 AN: 5156

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4816

European-Finnish (FIN) AF: 0.275 AC: 2902 AN: 10560

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19995 AN: 67974

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.381 Hom.: 1703

Bravo AF: 0.457

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-0.72
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: rs1680785; hg19: chr3-128644816;