X-42273924-T-C

Variant names:

• chrX-42273924-T-C
• rs4509495
• ENST00000411879.5:n.193+19116T>C

Variant summary

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

The ENST00000411879.5(ENSG00000231772):​n.193+19116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 109,791 control chromosomes in the GnomAD database, including 8,215 homozygotes. There are 10,813 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 0.36 (8215 hom., 10813 hem., cov: 21)
• Consequence: ENSG00000231772 ENST00000411879.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 0 publications found

Genes affected

ENSG00000231772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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
ENSG00000231772	ENST00000411879.5	n.193+19116T>C		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 39226 AN: 109739 Hom.: 8206 Cov.: 21

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.0643

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.358 AC: 39291 AN: 109791 Hom.: 8215 Cov.: 21 AF XY: 0.337 AC XY: 10813 AN XY: 32103

African (AFR) AF: 0.793 AC: 23702 AN: 29905

American (AMR) AF: 0.267 AC: 2758 AN: 10315

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 470 AN: 2629

East Asian (EAS) AF: 0.165 AC: 569 AN: 3453

South Asian (SAS) AF: 0.184 AC: 471 AN: 2556

European-Finnish (FIN) AF: 0.172 AC: 1006 AN: 5840

Middle Eastern (MID) AF: 0.255 AC: 54 AN: 212

European-Non Finnish (NFE) AF: 0.184 AC: 9704 AN: 52693

Other (OTH) AF: 0.341 AC: 513 AN: 1504

Alfa AF: 0.355 Hom.: 3191

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4509495; hg19: chrX-42133177;