7-21606637-C-T

Variant names:

• chr7-21606637-C-T
• rs886038464
• NM_001277115.2:c.3766-10C>T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001277115.2(DNAH11):​c.3766-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0013 (0 hom., cov: 16)
  • Exomes 𝑓: 0.000029 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DNAH11 NM_001277115.2 intron
• Scores: Splicing: ADA: 0.00003773
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2	c.3766-10C>T		intron_variant	Intron 19 of 81	ENST00000409508.8	NP_001264044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8	c.3766-10C>T		intron_variant	Intron 19 of 81	5	NM_001277115.2	ENSP00000475939.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 88 AN: 67958 Hom.: 0 Cov.: 16 FAILED QC

Gnomad AFR AF: 0.000850

Gnomad AMI AF: 0.00214

Gnomad AMR AF: 0.00168

Gnomad ASJ AF: 0.000992

Gnomad EAS AF: 0.00103

Gnomad SAS AF: 0.000421

Gnomad FIN AF: 0.00410

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00129

Gnomad OTH AF: 0.00119

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000293 AC: 22 AN: 749636 Hom.: 0 Cov.: 24 AF XY: 0.0000371 AC XY: 14 AN XY: 377630

Gnomad4 AFR exome AF: 0.0000561

Gnomad4 AMR exome AF: 0.000270

Gnomad4 ASJ exome AF: 0.000134

Gnomad4 EAS exome AF: 0.0000756

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000308

Gnomad4 NFE exome AF: 0.0000162

Gnomad4 OTH exome AF: 0.0000290

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00129 AC: 88 AN: 68000 Hom.: 0 Cov.: 16 AF XY: 0.00135 AC XY: 43 AN XY: 31768

Gnomad4 AFR AF: 0.000847

Gnomad4 AMR AF: 0.00167

Gnomad4 ASJ AF: 0.000992

Gnomad4 EAS AF: 0.00103

Gnomad4 SAS AF: 0.000423

Gnomad4 FIN AF: 0.00410

Gnomad4 NFE AF: 0.00129

Gnomad4 OTH AF: 0.00118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.24
DANN	Benign	0.13

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000038
dbscSNV1_RF	Benign	0.0060
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: rs886038464; hg19: chr7-21646255;