rs7057635

Variant names:

• chrX-152163253-T-A
• rs7057635
• ENST00000453915.1:n.110-944T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000453915.1(ENSG00000231937):​n.110-944T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0118 in 112,588 control chromosomes in the GnomAD database, including 23 homozygotes. There are 359 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 0.012 (23 hom., 359 hem., cov: 23)
• Consequence: ENSG00000231937 ENST00000453915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.993
• Publications: 1 publications found

Genes affected

ENSG00000231937 (HGNC:58378):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0118 (1324/112588) while in subpopulation AFR AF = 0.0403 (1252/31046). AF 95% confidence interval is 0.0385. There are 23 homozygotes in GnomAd4. There are 359 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 23 gene

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
ENSG00000231937	ENST00000453915.1	n.110-944T>A		intron_variant	Intron 2 of 3	5
ENSG00000231937	ENST00000778019.1	n.304-944T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0118 AC: 1323 AN: 112534 Hom.: 23 Cov.: 23

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00536

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000938

Gnomad OTH AF: 0.00663

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

GnomAD4 genome AF: 0.0118 AC: 1324 AN: 112588 Hom.: 23 Cov.: 23 AF XY: 0.0103 AC XY: 359 AN XY: 34762

African (AFR) AF: 0.0403 AC: 1252 AN: 31046

American (AMR) AF: 0.00535 AC: 57 AN: 10649

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2658

East Asian (EAS) AF: 0.00 AC: 0 AN: 3567

South Asian (SAS) AF: 0.00 AC: 0 AN: 2711

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6211

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.0000938 AC: 5 AN: 53318

Other (OTH) AF: 0.00655 AC: 10 AN: 1527

Alfa AF: 0.0102 Hom.: 29

Bravo AF: 0.0135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs7057635; hg19: chrX-151331725;