3-52347849-A-T

Variant names:

• chr3-52347849-A-T
• NM_015512.5:c.1981A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015512.5(DNAH1):​c.1981A>T​(p.Met661Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,446,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict 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: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: DNAH1 NM_015512.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

DNAH1 (HGNC:2940): (dynein axonemal heavy chain 1) This gene encodes an inner dynein arm heavy chain that provides structural support between the radial spokes and the outer doublet of the sperm tail. Naturally occurring mutations in this gene are associated with primary ciliary dyskinesia and multiple morphological anomalies of the flagella that result in asthenozoospermia and male infertility. Mice with a homozygous knockout of the orthologous gene are viable but have reduced sperm motility and are infertile. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.056832552).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH1	NM_015512.5	c.1981A>T	p.Met661Leu	missense_variant	Exon 12 of 78	ENST00000420323.7	NP_056327.4
DNAH1	XM_017006129.2	c.1981A>T	p.Met661Leu	missense_variant	Exon 13 of 80		XP_016861618.1
DNAH1	XM_017006130.2	c.1981A>T	p.Met661Leu	missense_variant	Exon 13 of 79		XP_016861619.1
DNAH1	XM_017006131.2	c.1981A>T	p.Met661Leu	missense_variant	Exon 13 of 79		XP_016861620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH1	ENST00000420323.7	c.1981A>T	p.Met661Leu	missense_variant	Exon 12 of 78	1	NM_015512.5	ENSP00000401514.2
DNAH1	ENST00000486752.5	n.2242A>T		non_coding_transcript_exon_variant	Exon 12 of 77	2
DNAH1	ENST00000497875.1	n.2146A>T		non_coding_transcript_exon_variant	Exon 13 of 21	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.91e-7 AC: 1 AN: 1446812 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 717938

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.06e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.099
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.51
Eigen	Benign	-1.1
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.35	N
LIST_S2	Benign	0.21	T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.057	T
MetaSVM	Benign	-0.96	T
PrimateAI	Benign	0.35	T
PROVEAN	Benign	0.17	N
REVEL	Benign	0.026
Sift	Benign	0.83	T
Sift4G	Benign	0.78	T
Vest4		0.20
MutPred		0.47		Loss of stability (P = 0.0467);
MVP		0.092
MPC		0.12
ClinPred		0.025	T
GERP RS		3.1
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-52381865;