rs408986

Variant names:

• chr1-36086294-A-G
• rs408986
• NM_014466.3:c.488+253A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-36086294-A-G
• chr1-36086294-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_014466.3(TEKT2):​c.488+253A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,128 control chromosomes in the GnomAD database, including 64,700 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.92 (64700 hom., cov: 30)
• Consequence: TEKT2 NM_014466.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

Genes affected

TEKT2 (HGNC:11725): (tektin 2) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. This gene is expressed in the testis and its protein is localized to the flagella of the sperms, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 1-36086294-A-G is Benign according to our data. Variant chr1-36086294-A-G is described in ClinVar as Benign. ClinVar VariationId is 1266573.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014466.3. 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
	TEKT2	NM_014466.3	MANE Select	c.488+253A>G		intron	N/A	NP_055281.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT2	ENST00000207457.8	TSL:1 MANE Select	c.488+253A>G		intron	N/A	ENSP00000207457.3	Q9UIF3
	TEKT2	ENST00000902746.1		c.488+253A>G		intron	N/A	ENSP00000572805.1
	TEKT2	ENST00000922202.1		c.488+253A>G		intron	N/A	ENSP00000592261.1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140092 AN: 152010 Hom.: 64643 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.922 AC: 140207 AN: 152128 Hom.: 64700 Cov.: 30 AF XY: 0.922 AC XY: 68536 AN XY: 74352

African (AFR) AF: 0.920 AC: 38169 AN: 41506

American (AMR) AF: 0.945 AC: 14447 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3103 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5149 AN: 5154

South Asian (SAS) AF: 0.918 AC: 4424 AN: 4820

European-Finnish (FIN) AF: 0.897 AC: 9492 AN: 10586

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62332 AN: 67988

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.908 Hom.: 5291

Bravo AF: 0.924

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.31
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs408986; hg19: chr1-36551895;