X-27114257-T-C

Variant names:

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

Variant summary

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

The ENST00000609836.1(ENSG00000228933):​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: ENSG00000228933 ENST00000609836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 3 publications found

Genes affected

ENSG00000228933 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000228933	ENST00000609836.1	n.89+44648A>G		intron_variant	Intron 1 of 1	3
ENSG00000228933	ENST00000717233.1	n.1016+44648A>G		intron_variant	Intron 9 of 10
ENSG00000228933	ENST00000717234.1	n.1154+44648A>G		intron_variant	Intron 10 of 11

Frequencies

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

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

African (AFR) AF: 0.335 AC: 10199 AN: 30489

American (AMR) AF: 0.473 AC: 4904 AN: 10370

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1196 AN: 2609

East Asian (EAS) AF: 0.694 AC: 2398 AN: 3453

South Asian (SAS) AF: 0.552 AC: 1446 AN: 2621

European-Finnish (FIN) AF: 0.479 AC: 2770 AN: 5784

Middle Eastern (MID) AF: 0.425 AC: 90 AN: 212

European-Non Finnish (NFE) AF: 0.469 AC: 24706 AN: 52661

Other (OTH) AF: 0.434 AC: 649 AN: 1494

Alfa AF: 0.459 Hom.: 26319

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1037193; hg19: chrX-27132374;