rs5981378

Positions:

• chrX-75608136-C-T

Variant summary

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

The XR_007068273.1(LOC107985664):​n.633+3114C>T 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 0.0751 in 111,876 control chromosomes in the GnomAD database, including 459 homozygotes. There are 2,295 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 0.075 (459 hom., 2295 hem., cov: 22)
• Consequence: LOC107985664 XR_007068273.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

LOC107985664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985664	XR_007068273.1	n.633+3114C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 8368 AN: 111824 Hom.: 456 Cov.: 22 AF XY: 0.0667 AC XY: 2269 AN XY: 34026

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0168

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0576

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

GnomAD4 genome AF: 0.0751 AC: 8405 AN: 111876 Hom.: 459 Cov.: 22 AF XY: 0.0673 AC XY: 2295 AN XY: 34088

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0272

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0355 Hom.: 2296

Bravo AF: 0.0814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5981378; hg19: chrX-74827971;