chr2-145228950-G-A

Variant names:

• chr2-145228950-G-A
• rs1822620
• ENST00000629218.2:n.621+3978G>A

Variant summary

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

The ENST00000629218.2(TEX41):​n.621+3978G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,188 control chromosomes in the GnomAD database, including 296 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 0.042 (296 hom., cov: 32)
• Consequence: TEX41 ENST00000629218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 3 publications found

Genes affected

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

LOC100505498 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629218.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000629218.2	TSL:5	n.621+3978G>A		intron	N/A
	TEX41	ENST00000630139.2	TSL:5	n.536-30236G>A		intron	N/A
	TEX41	ENST00000762903.1		n.157-30236G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6344 AN: 152070 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0417 AC: 6349 AN: 152188 Hom.: 296 Cov.: 32 AF XY: 0.0400 AC XY: 2974 AN XY: 74424

African (AFR) AF: 0.112 AC: 4662 AN: 41484

American (AMR) AF: 0.0354 AC: 542 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00664 AC: 23 AN: 3466

East Asian (EAS) AF: 0.0432 AC: 224 AN: 5186

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4826

European-Finnish (FIN) AF: 0.00189 AC: 20 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 684 AN: 68014

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0231 Hom.: 329

Bravo AF: 0.0469

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1822620; hg19: chr2-145986518;