rs557373

Positions:

• chr6-44290587-G-A
• chr6-44290587-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182539.4(TCTE1):​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: TCTE1 NM_182539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

TCTE1 (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]

POLR1C (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCTE1	NM_182539.4	c.-93-2669C>T		intron_variant		ENST00000371505.5	NP_872345.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCTE1	ENST00000371505.5	c.-93-2669C>T		intron_variant		1	NM_182539.4	ENSP00000360560	P1
TMEM151B	ENST00000438774.2	c.577-16356G>A		intron_variant		3		ENSP00000409337

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

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.724

Alfa AF: 0.760 Hom.: 5587

Bravo AF: 0.703

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.53
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs557373; hg19: chr6-44258324;