16-57698010-G-T

Variant names:

• chr16-57698010-G-T
• rs147737491
• NM_001289162.2:c.61G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001289162.2(DRC7):​c.61G>T​(p.Glu21*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DRC7 NM_001289162.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56
• Publications: 1 publications found

Genes affected

DRC7 (HGNC:25289): (dynein regulatory complex subunit 7) Predicted to be involved in flagellated sperm motility. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000260467 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001289162.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRC7	NM_001289162.2	MANE Select	c.61G>T	p.Glu21*	stop_gained	Exon 3 of 19	NP_001276091.1	Q8IY82-1
	DRC7	NM_032269.6		c.61G>T	p.Glu21*	stop_gained	Exon 2 of 18	NP_115645.4
	DRC7	NM_001289163.2		c.61G>T	p.Glu21*	stop_gained	Exon 2 of 17	NP_001276092.1	Q8IY82-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRC7	ENST00000360716.8	TSL:1 MANE Select	c.61G>T	p.Glu21*	stop_gained	Exon 3 of 19	ENSP00000353942.3	Q8IY82-1
	DRC7	ENST00000394337.8	TSL:1	c.61G>T	p.Glu21*	stop_gained	Exon 2 of 18	ENSP00000377869.4	Q8IY82-1
	DRC7	ENST00000871948.1		c.61G>T	p.Glu21*	stop_gained	Exon 3 of 19	ENSP00000542007.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Uncertain	0.34
Eigen_PC	Benign	0.032
FATHMM_MKL	Benign	0.46	N
PhyloP100		2.6
Vest4		0.20
GERP RS		3.0

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: rs147737491; hg19: chr16-57731922;