chrX-100578978-T-C

Variant names:

• chrX-100578978-T-C
• rs873275
• ENST00000780746.1:n.77+27216A>G

Variant summary

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

The ENST00000780746.1(ENSG00000301679):​n.77+27216A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 111,473 control chromosomes in the GnomAD database, including 1,456 homozygotes. There are 5,588 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 0.17 (1456 hom., 5588 hem., cov: 23)
• Consequence: ENSG00000301679 ENST00000780746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 2 publications found

Genes affected

ENSG00000301679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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
ENSG00000301679	ENST00000780746.1	n.77+27216A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 19036 AN: 111421 Hom.: 1456 Cov.: 23

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00280

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.171 AC: 19036 AN: 111473 Hom.: 1456 Cov.: 23 AF XY: 0.166 AC XY: 5588 AN XY: 33705

African (AFR) AF: 0.0677 AC: 2081 AN: 30752

American (AMR) AF: 0.189 AC: 1986 AN: 10507

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 622 AN: 2646

East Asian (EAS) AF: 0.00281 AC: 10 AN: 3565

South Asian (SAS) AF: 0.127 AC: 337 AN: 2658

European-Finnish (FIN) AF: 0.257 AC: 1522 AN: 5927

Middle Eastern (MID) AF: 0.167 AC: 36 AN: 215

European-Non Finnish (NFE) AF: 0.227 AC: 12057 AN: 53002

Other (OTH) AF: 0.138 AC: 210 AN: 1526

Alfa AF: 0.192 Hom.: 7279

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.83
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs873275; hg19: chrX-99833975;