rs1822620

Positions:

• chr2-145228950-G-A

Variant summary

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

The XR_923410.3(LOC100505498):​n.10795-30236G>A variant causes a intron, non coding transcript 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: LOC100505498 XR_923410.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

LOC100505498 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100505498	XR_923410.3	n.10795-30236G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX41	ENST00000629218.2	n.621+3978G>A		intron_variant, non_coding_transcript_variant		5
TEX41	ENST00000630139.2	n.536-30236G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.00664

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.00189

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0156 Hom.: 93

Bravo AF: 0.0469

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822620; hg19: chr2-145986518;