chr7-21900939-AACTT-A

Position:

• chr7-21900939-AACTT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018719.5(CDCA7L):​c.*1379_*1382del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 1,502,682 control chromosomes in the GnomAD database, including 671,147 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.86 (57323 hom., cov: 0)
  • Exomes 𝑓: 0.95 (613824 hom.)
• Consequence: CDCA7L NM_018719.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0560

Genes affected

CDCA7L (HGNC:30777): (cell division cycle associated 7 like) Acts upstream of or within positive regulation of cell population proliferation. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-21900939-AACTT-A is Benign according to our data. Variant chr7-21900939-AACTT-A is described in ClinVar as [Benign]. Clinvar id is 1251756.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDCA7L	NM_018719.5	c.*1379_*1382del		3_prime_UTR_variant	10/10	ENST00000406877.8	NP_061189.2
DNAH11	NM_001277115.2	c.13304-63_13304-60del		intron_variant		ENST00000409508.8	NP_001264044.1
CDCA7L	NM_001127370.3	c.*1379_*1382del		3_prime_UTR_variant	11/11		NP_001120842.1
CDCA7L	NM_001127371.3	c.*1379_*1382del		3_prime_UTR_variant	9/9		NP_001120843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDCA7L	ENST00000406877.8	c.*1379_*1382del		3_prime_UTR_variant	10/10	1	NM_018719.5	ENSP00000383986	P1
DNAH11	ENST00000409508.8	c.13304-63_13304-60del		intron_variant		5	NM_001277115.2	ENSP00000475939	P1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130069 AN: 151760 Hom.: 57318 Cov.: 0

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.871

GnomAD4 exome AF: 0.950 AC: 1283108 AN: 1350806 Hom.: 613824 AF XY: 0.949 AC XY: 626873 AN XY: 660316

Gnomad4 AFR exome AF: 0.647

Gnomad4 AMR exome AF: 0.710

Gnomad4 ASJ exome AF: 0.946

Gnomad4 EAS exome AF: 0.714

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.978

Gnomad4 NFE exome AF: 0.978

Gnomad4 OTH exome AF: 0.927

GnomAD4 genome AF: 0.857 AC: 130123 AN: 151876 Hom.: 57323 Cov.: 0 AF XY: 0.855 AC XY: 63433 AN XY: 74222

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.871

Alfa AF: 0.910 Hom.: 7792

Bravo AF: 0.829

Asia WGS AF: 0.774 AC: 2690 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 04, 2020

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs10555456; hg19: chr7-21940557;