chrX-27114257-T-C

Variant names:

• chrX-27114257-T-C
• rs1037193
• ENST00000609836.1:n.89+44648A>G

Variant summary

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

The ENST00000609836.1(ENSG00000242021):​n.89+44648A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 110,369 control chromosomes in the GnomAD database, including 7,814 homozygotes. There are 14,432 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 0.44 (7814 hom., 14432 hem., cov: 23)
• Consequence: ENSG00000242021 ENST00000609836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

ENSG00000242021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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
ENSG00000242021	ENST00000609836.1	n.89+44648A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 48779 AN: 110318 Hom.: 7817 Cov.: 23 AF XY: 0.442 AC XY: 14411 AN XY: 32568

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.442 AC: 48791 AN: 110369 Hom.: 7814 Cov.: 23 AF XY: 0.442 AC XY: 14432 AN XY: 32629

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.434

Alfa AF: 0.466 Hom.: 20254

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037193; hg19: chrX-27132374;