chr6-44290587-G-A

Variant names:

• chr6-44290587-G-A
• rs557373
• NM_182539.4:c.-93-2669C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182539.4(DRC5):​c.-93-2669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,040 control chromosomes in the GnomAD database, including 39,902 homozygotes. 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 0.71 (39902 hom., cov: 32)
• Consequence: DRC5 NM_182539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

Genes affected

DRC5 (HGNC:11693): (t-complex-associated-testis-expressed 1) Predicted to be involved in flagellated sperm motility. Predicted to be located in sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272442 (HGNC:):

TMEM151B (HGNC:21315): (transmembrane protein 151B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182539.4. 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
	DRC5	NM_182539.4	MANE Select	c.-93-2669C>T		intron	N/A	NP_872345.2	Q5JU00

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCTE1	ENST00000371505.5	TSL:1 MANE Select	c.-93-2669C>T		intron	N/A	ENSP00000360560.4	Q5JU00
	ENSG00000272442	ENST00000505802.1	TSL:2	n.313-16356G>A		intron	N/A	ENSP00000424257.1	H0Y9J4
	TCTE1	ENST00000897136.1		c.-93-2669C>T		intron	N/A	ENSP00000567195.1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108320 AN: 151922 Hom.: 39880 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.713 AC: 108382 AN: 152040 Hom.: 39902 Cov.: 32 AF XY: 0.711 AC XY: 52852 AN XY: 74308

African (AFR) AF: 0.518 AC: 21469 AN: 41410

American (AMR) AF: 0.793 AC: 12119 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2657 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3055 AN: 5152

South Asian (SAS) AF: 0.697 AC: 3358 AN: 4820

European-Finnish (FIN) AF: 0.774 AC: 8194 AN: 10584

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55027 AN: 67998

Other (OTH) AF: 0.724 AC: 1530 AN: 2114

Alfa AF: 0.751 Hom.: 5693

Bravo AF: 0.703

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.53
DANN	Benign	0.33
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs557373; hg19: chr6-44258324;