chr17-43784923-G-A

Variant names:

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

Variant summary

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

The NM_001136483.3(CFAP97D1):​c.*541G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 152,036 control chromosomes in the GnomAD database, including 416 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 0.041 (416 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

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>A		3_prime_UTR	Exon 6 of 6	NP_001129955.1
	CFAP97D1	NM_001353400.2		c.*417G>A		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>A		3_prime_UTR	Exon 6 of 6	ENSP00000415662.2
	ENSG00000267604	ENST00000591540.1	TSL:3	n.-241C>T		upstream_gene	N/A
	CFAP97D1	ENST00000590148.1	TSL:4	n.*435G>A		downstream_gene	N/A	ENSP00000468141.1

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6210 AN: 151918 Hom.: 417 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.000838

Gnomad OTH AF: 0.0287

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0409 AC: 6223 AN: 152036 Hom.: 416 Cov.: 31 AF XY: 0.0391 AC XY: 2907 AN XY: 74344

African (AFR) AF: 0.141 AC: 5834 AN: 41414

American (AMR) AF: 0.0152 AC: 232 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10586

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.000838 AC: 57 AN: 68006

Other (OTH) AF: 0.0284 AC: 60 AN: 2110

Alfa AF: 0.0295 Hom.: 29

Bravo AF: 0.0466

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.50
DANN	Benign	0.41
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;