chr7-21788462-C-T

Position:

• chr7-21788462-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277115.2(DNAH11):​c.9925-779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,682 control chromosomes in the GnomAD database, including 1,551 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 0.13 (1551 hom., cov: 32)
• Consequence: DNAH11 NM_001277115.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH11	NM_001277115.2	c.9925-779C>T		intron_variant		ENST00000409508.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH11	ENST00000409508.8	c.9925-779C>T		intron_variant		5	NM_001277115.2	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18951 AN: 151562 Hom.: 1548 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0708

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.129

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.125 AC: 18967 AN: 151682 Hom.: 1551 Cov.: 32 AF XY: 0.126 AC XY: 9345 AN XY: 74104

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.0708

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0884 Hom.: 949

Bravo AF: 0.131

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.62

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: rs10248618; hg19: chr7-21828080;