chr11-6501574-G-C

Variant names:

• chr11-6501574-G-C
• rs2555155
• NM_144666.3:c.747-1179G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144666.3(DNHD1):​c.747-1179G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
• Consequence: DNHD1 NM_144666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 0 publications found

Genes affected

DNHD1 (HGNC:26532): (dynein heavy chain domain 1) Predicted to enable dynein intermediate chain binding activity; dynein light intermediate chain binding activity; and minus-end-directed microtubule motor activity. Predicted to be involved in cilium movement. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

DNHD1 Gene-Disease associations (from GenCC):

• spermatogenic failure 65

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000283977 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNHD1	NM_144666.3	c.747-1179G>C		intron_variant	Intron 3 of 42	ENST00000254579.11	NP_653267.2
DNHD1	NM_173589.4	c.747-1179G>C		intron_variant	Intron 2 of 7		NP_775860.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNHD1	ENST00000254579.11	c.747-1179G>C		intron_variant	Intron 3 of 42	5	NM_144666.3	ENSP00000254579.6
DNHD1	ENST00000354685.7	c.747-1179G>C		intron_variant	Intron 2 of 7	1		ENSP00000346716.3
DNHD1	ENST00000473019.5	n.395-1179G>C		intron_variant	Intron 3 of 3	2
ENSG00000283977	ENST00000639224.1	n.*69-1179G>C		intron_variant	Intron 2 of 3	4		ENSP00000492738.1

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-0.64

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: rs2555155; hg19: chr11-6522804;