chr2-144934149-G-A

Variant names:

• chr2-144934149-G-A
• rs786255
• ENST00000445791.5:n.308-136671G>A

Variant summary

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

The ENST00000445791.5(TEX41):​n.308-136671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,862 control chromosomes in the GnomAD database, including 27,821 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 0.60 (27821 hom., cov: 32)
• Consequence: TEX41 ENST00000445791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445791.5. 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
	TEX41	NR_033870.2		n.463+30346G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000445791.5	TSL:1	n.308-136671G>A		intron	N/A
	TEX41	ENST00000451774.5	TSL:1	n.404+30346G>A		intron	N/A
	TEX41	ENST00000451027.5	TSL:4	n.469-110217G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90523 AN: 151742 Hom.: 27809 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.596 AC: 90565 AN: 151862 Hom.: 27821 Cov.: 32 AF XY: 0.602 AC XY: 44678 AN XY: 74200

African (AFR) AF: 0.484 AC: 20030 AN: 41404

American (AMR) AF: 0.660 AC: 10058 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5052 AN: 5168

South Asian (SAS) AF: 0.719 AC: 3465 AN: 4820

European-Finnish (FIN) AF: 0.615 AC: 6465 AN: 10510

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41176 AN: 67950

Other (OTH) AF: 0.573 AC: 1210 AN: 2112

Alfa AF: 0.600 Hom.: 3478

Bravo AF: 0.595

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.56
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs786255; hg19: chr2-145691716;