16-57702036-A-T

Variant names:

• chr16-57702036-A-T
• rs571695768
• NM_001289162.2:c.605A>T

Variant summary

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

The NM_001289162.2(DRC7):​c.605A>T​(p.Tyr202Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y202C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DRC7 NM_001289162.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.76
• Publications: 0 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]

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.605A>T	p.Tyr202Phe	missense	Exon 6 of 19	NP_001276091.1	Q8IY82-1
	DRC7	NM_032269.6		c.605A>T	p.Tyr202Phe	missense	Exon 5 of 18	NP_115645.4
	DRC7	NM_001289163.2		c.504+1766A>T		intron	N/A	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.605A>T	p.Tyr202Phe	missense	Exon 6 of 19	ENSP00000353942.3	Q8IY82-1
	DRC7	ENST00000394337.8	TSL:1	c.605A>T	p.Tyr202Phe	missense	Exon 5 of 18	ENSP00000377869.4	Q8IY82-1
	DRC7	ENST00000871948.1		c.605A>T	p.Tyr202Phe	missense	Exon 6 of 19	ENSP00000542007.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.091	T
BayesDel_noAF	Benign	-0.37
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Benign	0.19	T
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.93	D
M_CAP	Benign	0.070	D
MetaRNN	Uncertain	0.72	D
MetaSVM	Benign	-1.0	T
PhyloP100		6.8
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-2.8	D
REVEL	Uncertain	0.33
Sift	Benign	0.15	T
Sift4G	Benign	0.082	T
Polyphen		1.0	D
Vest4		0.75
MutPred		0.58		Gain of helix (P = 0.132)
MVP		0.46
MPC		0.67
ClinPred		0.98	D
GERP RS		5.0
Varity_R		0.23
gMVP		0.76

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: rs571695768; hg19: chr16-57735948;