rs312965

Positions:

• chr2-21136956-G-A
• chr2-21136956-G-C
• chr2-21136956-G-T

Variant summary

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

The NM_001306137.2(TDRD15):​c.-3-509G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 152,058 control chromosomes in the GnomAD database, including 69,222 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 0.95 (69222 hom., cov: 32)
• Consequence: TDRD15 NM_001306137.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

Genes affected

TDRD15 (HGNC:45037): (tudor domain containing 15)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TDRD15	NM_001306137.2	c.-3-509G>A		intron_variant		ENST00000405799.3
TDRD15	XM_011533212.2	c.-3-509G>A		intron_variant
TDRD15	XR_001738578.2	n.277-509G>A		intron_variant, non_coding_transcript_variant
TDRD15	XR_939798.3	n.277-509G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TDRD15	ENST00000405799.3	c.-3-509G>A		intron_variant		2	NM_001306137.2	P1

Frequencies

GnomAD3 genomes AF: 0.954 AC: 144939 AN: 151940 Hom.: 69164 Cov.: 32

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.962

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

GnomAD4 genome AF: 0.954 AC: 145056 AN: 152058 Hom.: 69222 Cov.: 32 AF XY: 0.954 AC XY: 70936 AN XY: 74352

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.962

Alfa AF: 0.954 Hom.: 71241

Bravo AF: 0.959

Asia WGS AF: 0.993 AC: 3453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.55

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: rs312965; hg19: chr2-21359828;