X-76127599-G-A

Variant names:

• chrX-76127599-G-A
• rs5937496
• ENST00000844515.1:n.355-12965C>T

Variant summary

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

The ENST00000844515.1(ENSG00000309870):​n.355-12965C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 111,321 control chromosomes in the GnomAD database, including 1,059 homozygotes. There are 4,743 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 0.15 (1059 hom., 4743 hem., cov: 23)
• Consequence: ENSG00000309870 ENST00000844515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 3 publications found

Genes affected

ENSG00000309870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844515.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309870	ENST00000844515.1		n.355-12965C>T		intron	N/A
	ENSG00000309870	ENST00000844516.1		n.279-12965C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 17196 AN: 111268 Hom.: 1058 Cov.: 23

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00761

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.155 AC: 17202 AN: 111321 Hom.: 1059 Cov.: 23 AF XY: 0.141 AC XY: 4743 AN XY: 33565

African (AFR) AF: 0.199 AC: 6073 AN: 30587

American (AMR) AF: 0.103 AC: 1082 AN: 10509

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 373 AN: 2626

East Asian (EAS) AF: 0.00763 AC: 27 AN: 3539

South Asian (SAS) AF: 0.0877 AC: 232 AN: 2644

European-Finnish (FIN) AF: 0.130 AC: 777 AN: 5994

Middle Eastern (MID) AF: 0.137 AC: 29 AN: 212

European-Non Finnish (NFE) AF: 0.157 AC: 8297 AN: 53016

Other (OTH) AF: 0.154 AC: 234 AN: 1521

Alfa AF: 0.157 Hom.: 11645

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.54
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs5937496; hg19: chrX-75347434;