chrX-69371091-G-A

Variant names:

• chrX-69371091-G-A
• rs10521345
• ENST00000848419.1:n.383+4468G>A

Variant summary

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

The ENST00000848419.1(ENSG00000310220):​n.383+4468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 112,263 control chromosomes in the GnomAD database, including 476 homozygotes. There are 3,109 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 0.093 (476 hom., 3109 hem., cov: 23)
• Consequence: ENSG00000310220 ENST00000848419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 0 publications found

Genes affected

ENSG00000310220 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310220	ENST00000848419.1	n.383+4468G>A		intron_variant	Intron 2 of 2
ENSG00000310220	ENST00000848420.1	n.249+7703G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 10414 AN: 112209 Hom.: 472 Cov.: 23

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0717

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0930 AC: 10435 AN: 112263 Hom.: 476 Cov.: 23 AF XY: 0.0903 AC XY: 3109 AN XY: 34445

African (AFR) AF: 0.151 AC: 4660 AN: 30823

American (AMR) AF: 0.0740 AC: 788 AN: 10642

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 282 AN: 2652

East Asian (EAS) AF: 0.330 AC: 1168 AN: 3539

South Asian (SAS) AF: 0.194 AC: 531 AN: 2731

European-Finnish (FIN) AF: 0.0192 AC: 118 AN: 6153

Middle Eastern (MID) AF: 0.0741 AC: 16 AN: 216

European-Non Finnish (NFE) AF: 0.0511 AC: 2720 AN: 53281

Other (OTH) AF: 0.0942 AC: 145 AN: 1539

Alfa AF: 0.0757 Hom.: 4232

Bravo AF: 0.0977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.33
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10521345; hg19: chrX-68590934;