rs2301682

Variant names:

• chr17-43780658-G-T
• rs2301682
• NM_001136483.3:c.124+72G>T

Variant summary

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

The NM_001136483.3(CFAP97D1):​c.124+72G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 1,513,158 control chromosomes in the GnomAD database, including 5,799 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 0.10 (979 hom., cov: 32)
  • Exomes 𝑓: 0.081 (4820 hom.)
• Consequence: CFAP97D1 NM_001136483.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 9 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D1	NM_001136483.3	MANE Select	c.124+72G>T		intron	N/A	NP_001129955.1
	CFAP97D1	NM_001353400.2		c.124+72G>T		intron	N/A	NP_001340329.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D1	ENST00000449302.8	TSL:1 MANE Select	c.124+72G>T		intron	N/A	ENSP00000415662.2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15419 AN: 152114 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.0814 AC: 110776 AN: 1360926 Hom.: 4820 AF XY: 0.0824 AC XY: 55370 AN XY: 671972

African (AFR) AF: 0.182 AC: 5573 AN: 30612

American (AMR) AF: 0.0742 AC: 2588 AN: 34860

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 2203 AN: 24412

East Asian (EAS) AF: 0.125 AC: 4418 AN: 35458

South Asian (SAS) AF: 0.114 AC: 8787 AN: 77228

European-Finnish (FIN) AF: 0.0343 AC: 1640 AN: 47822

Middle Eastern (MID) AF: 0.155 AC: 866 AN: 5604

European-Non Finnish (NFE) AF: 0.0756 AC: 79235 AN: 1048288

Other (OTH) AF: 0.0965 AC: 5466 AN: 56642

GnomAD4 genome AF: 0.101 AC: 15434 AN: 152232 Hom.: 979 Cov.: 32 AF XY: 0.0986 AC XY: 7336 AN XY: 74438

African (AFR) AF: 0.169 AC: 7000 AN: 41522

American (AMR) AF: 0.0784 AC: 1200 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.137 AC: 709 AN: 5182

South Asian (SAS) AF: 0.113 AC: 543 AN: 4824

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10610

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5017 AN: 68006

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0881 Hom.: 457

Bravo AF: 0.111

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.69
PhyloP100		-2.1
PromoterAI		-0.078	Neutral
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: rs2301682; hg19: chr17-41858026;