chr17-43784923-G-C

Variant names:

• chr17-43784923-G-C
• rs41455049
• NM_001136483.3:c.*541G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001136483.3(CFAP97D1):​c.*541G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: CFAP97D1 NM_001136483.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 2 publications found

Genes affected

CFAP97D1 (HGNC:37241): (CFAP97 domain containing 1) Predicted to be involved in sperm axoneme assembly. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267604 (HGNC:58321):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136483.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D1	NM_001136483.3	MANE Select	c.*541G>C		3_prime_UTR	Exon 6 of 6	NP_001129955.1
	CFAP97D1	NM_001353400.2		c.*417G>C		3_prime_UTR	Exon 5 of 5	NP_001340329.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D1	ENST00000449302.8	TSL:1 MANE Select	c.*541G>C		3_prime_UTR	Exon 6 of 6	ENSP00000415662.2
	ENSG00000267604	ENST00000591540.1	TSL:3	n.-241C>G		upstream_gene	N/A
	CFAP97D1	ENST00000590148.1	TSL:4	n.*435G>C		downstream_gene	N/A	ENSP00000468141.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.43
PhyloP100		-0.51

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: rs41455049; hg19: chr17-41862291;