X-75663162-T-G

Variant names:

• chrX-75663162-T-G
• rs5938152
• XR_001755892.2:n.821+38274T>G

Variant summary

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

The XR_001755892.2(LOC107985664):​n.821+38274T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 111,340 control chromosomes in the GnomAD database, including 193 homozygotes. There are 1,656 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 0.053 (193 hom., 1656 hem., cov: 23)
• Consequence: LOC107985664 XR_001755892.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

LOC107985664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985664	XR_001755892.2	n.821+38274T>G		intron_variant	Intron 3 of 3
LOC107985664	XR_001755894.2	n.821+38274T>G		intron_variant	Intron 3 of 3
LOC107985664	XR_007068272.1	n.957+38274T>G		intron_variant	Intron 4 of 4
LOC107985664	XR_007068273.1	n.821+38274T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 5898 AN: 111287 Hom.: 193 Cov.: 23 AF XY: 0.0491 AC XY: 1646 AN XY: 33511

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0299

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0168

Gnomad NFE AF: 0.0269

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0531 AC: 5915 AN: 111340 Hom.: 193 Cov.: 23 AF XY: 0.0493 AC XY: 1656 AN XY: 33574

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.0299

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0151

Gnomad4 NFE AF: 0.0269

Gnomad4 OTH AF: 0.0387

Alfa AF: 0.0412 Hom.: 648

Bravo AF: 0.0550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5938152; hg19: chrX-74882997;