rs16860868

Variant names:

• chr3-113361102-G-C
• rs16860868
• NM_001164496.2:c.2934+2043C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-113361102-G-C
• chr3-113361102-G-T

Variant summary

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

The NM_001164496.2(CFAP44):​c.2934+2043C>G variant causes a intron change. The variant allele was found at a frequency of 0.195 in 207,524 control chromosomes in the GnomAD database, including 4,697 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 0.18 (3121 hom., cov: 31)
  • Exomes 𝑓: 0.22 (1576 hom.)
• Consequence: CFAP44 NM_001164496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.47
• Publications: 4 publications found

Genes affected

CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Apr 2022]

RABGGTBP1 (HGNC:56479): (RABGGTB pseudogene 1)

SPICE1-CFAP44 (HGNC:58084):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP44	NM_001164496.2	c.2934+2043C>G		intron_variant	Intron 21 of 34	ENST00000393845.9	NP_001157968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9	c.2934+2043C>G		intron_variant	Intron 21 of 34	5	NM_001164496.2	ENSP00000377428.2
RABGGTBP1	ENST00000462549.1	n.836G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
CFAP44	ENST00000490481.1	n.165+2043C>G		intron_variant	Intron 1 of 3	5		ENSP00000419269.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28125 AN: 151950 Hom.: 3120 Cov.: 31

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.223 AC: 12345 AN: 55456 Hom.: 1576 Cov.: 0 AF XY: 0.225 AC XY: 7174 AN XY: 31822

African (AFR) AF: 0.0570 AC: 47 AN: 824

American (AMR) AF: 0.220 AC: 658 AN: 2988

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 192 AN: 1124

East Asian (EAS) AF: 0.411 AC: 660 AN: 1606

South Asian (SAS) AF: 0.265 AC: 2080 AN: 7844

European-Finnish (FIN) AF: 0.312 AC: 2429 AN: 7780

Middle Eastern (MID) AF: 0.140 AC: 32 AN: 228

European-Non Finnish (NFE) AF: 0.188 AC: 5747 AN: 30496

Other (OTH) AF: 0.195 AC: 500 AN: 2566

GnomAD4 genome AF: 0.185 AC: 28122 AN: 152068 Hom.: 3121 Cov.: 31 AF XY: 0.194 AC XY: 14443 AN XY: 74322

African (AFR) AF: 0.0812 AC: 3369 AN: 41502

American (AMR) AF: 0.213 AC: 3258 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2062 AN: 5152

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3529 AN: 10552

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13359 AN: 67970

Other (OTH) AF: 0.179 AC: 378 AN: 2112

Alfa AF: 0.112 Hom.: 202

Bravo AF: 0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		5.5
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: rs16860868; hg19: chr3-113079949;