rs10522040

chrX-36411364-C-T

Variant summary

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

The NR_110412.1(LOC101928627):n.1404+2551G>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 0.171 in 110,418 control chromosomes in the GnomAD database, including 3,600 homozygotes. There are 5,057 hemizygotes in GnomAD. 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 0.17 (3600 hom., 5057 hem., cov: 22)
• Consequence: LOC101928627 NR_110412.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928627	NR_110412.1	n.1404+2551G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000455438.2	n.1404+2551G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 18794 AN: 110373 Hom.: 3599 Cov.: 22 AF XY: 0.153 AC XY: 5019 AN XY: 32705

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0278

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.00228

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.00579

Gnomad MID AF: 0.0603

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.171 AC: 18839 AN: 110418 Hom.: 3600 Cov.: 22 AF XY: 0.154 AC XY: 5057 AN XY: 32760

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.00228

Gnomad4 EAS AF: 0.00113

Gnomad4 SAS AF: 0.0472

Gnomad4 FIN AF: 0.00579

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.123

Alfa AF: 0.107 Hom.: 727

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10522040; hg19: chrX-36429477;