rs17409319

Variant names:

• chr2-145245620-C-T
• rs17409319
• ENST00000629218.2:n.622-13566C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000762903.1(TEX41):​n.157-13566C>T variant causes a intron change. The variant allele was found at a frequency of 0.082 in 152,140 control chromosomes in the GnomAD database, including 575 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 0.082 (575 hom., cov: 32)
• Consequence: TEX41 ENST00000762903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.32
• Publications: 2 publications found

Genes affected

TEX41 (HGNC:48667): (testis expressed 41)

LOC100505498 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762903.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000629218.2	TSL:5	n.622-13566C>T		intron	N/A
	TEX41	ENST00000630139.2	TSL:5	n.536-13566C>T		intron	N/A
	TEX41	ENST00000762903.1		n.157-13566C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12474 AN: 152022 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0820 AC: 12482 AN: 152140 Hom.: 575 Cov.: 32 AF XY: 0.0845 AC XY: 6286 AN XY: 74352

African (AFR) AF: 0.0470 AC: 1952 AN: 41544

American (AMR) AF: 0.0930 AC: 1419 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3472

East Asian (EAS) AF: 0.0835 AC: 431 AN: 5160

South Asian (SAS) AF: 0.0774 AC: 373 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6222 AN: 67982

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0849 Hom.: 734

Bravo AF: 0.0776

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Uncertain	23
DANN	Benign	0.81
PhyloP100		4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17409319;

hg19: chr2-146003188;