XR_923410.3:n.7385A>G

Variant names:

• chr2-145183669-A-G
• rs274853
• XR_923410.3:n.7385A>G

Variant summary

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

The XR_923410.3(LOC100505498):​n.7385A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,178 control chromosomes in the GnomAD database, including 67,122 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 0.94 (67122 hom., cov: 31)
• Consequence: LOC100505498 XR_923410.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 1 publications found

Genes affected

LOC100505498 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100505498	XR_923410.3	n.7385A>G		non_coding_transcript_exon_variant	Exon 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX41	ENST00000625557.1	n.99-36696A>G		intron_variant	Intron 1 of 1	5
TEX41	ENST00000627545.2	n.181+11538A>G		intron_variant	Intron 2 of 2	5
TEX41	ENST00000628237.2	n.316-412A>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142208 AN: 152060 Hom.: 67086 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.935 AC: 142304 AN: 152178 Hom.: 67122 Cov.: 31 AF XY: 0.937 AC XY: 69685 AN XY: 74402

African (AFR) AF: 0.791 AC: 32824 AN: 41482

American (AMR) AF: 0.972 AC: 14842 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3436 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5130 AN: 5174

South Asian (SAS) AF: 0.965 AC: 4659 AN: 4826

European-Finnish (FIN) AF: 0.997 AC: 10561 AN: 10594

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67635 AN: 68034

Other (OTH) AF: 0.955 AC: 2020 AN: 2116

Alfa AF: 0.960 Hom.: 9057

Bravo AF: 0.927

Asia WGS AF: 0.967 AC: 3359 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.63
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs274853; hg19: chr2-145941236;