chrX-107001537-C-T

Variant names:

• chrX-107001537-C-T
• rs12688220
• ENST00000773597.1:n.146-1197C>T

Variant summary

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

The ENST00000773597.1(ENSG00000300720):​n.146-1197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 111,290 control chromosomes in the GnomAD database, including 1,997 homozygotes. There are 6,628 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 0.20 (1997 hom., 6628 hem., cov: 23)
• Consequence: ENSG00000300720 ENST00000773597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 30 publications found

Genes affected

ENSG00000300720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773597.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300720	ENST00000773597.1		n.146-1197C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 21847 AN: 111239 Hom.: 1996 Cov.: 23

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.196 AC: 21858 AN: 111290 Hom.: 1997 Cov.: 23 AF XY: 0.197 AC XY: 6628 AN XY: 33568

African (AFR) AF: 0.0455 AC: 1399 AN: 30761

American (AMR) AF: 0.200 AC: 2108 AN: 10530

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 499 AN: 2637

East Asian (EAS) AF: 0.354 AC: 1238 AN: 3500

South Asian (SAS) AF: 0.455 AC: 1197 AN: 2633

European-Finnish (FIN) AF: 0.250 AC: 1467 AN: 5866

Middle Eastern (MID) AF: 0.136 AC: 29 AN: 214

European-Non Finnish (NFE) AF: 0.256 AC: 13543 AN: 52948

Other (OTH) AF: 0.195 AC: 297 AN: 1521

Alfa AF: 0.223 Hom.: 13183

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs12688220; hg19: chrX-106244767;