rs7878993

Variant names:

• chrX-71180543-C-A
• rs7878993
• ENST00000740246.1:n.346+3368G>T

Variant summary

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

The ENST00000740246.1(ENSG00000228427):​n.346+3368G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 111,432 control chromosomes in the GnomAD database, including 7,474 homozygotes. There are 12,819 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 0.40 (7474 hom., 12819 hem., cov: 23)
• Consequence: ENSG00000228427 ENST00000740246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 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
ENSG00000228427	ENST00000740246.1	n.346+3368G>T		intron_variant	Intron 2 of 4
ENSG00000228427	ENST00000740247.1	n.367+3368G>T		intron_variant	Intron 2 of 3
ENSG00000228427	ENST00000740248.1	n.310+732G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 44466 AN: 111379 Hom.: 7474 Cov.: 23

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.399 AC: 44501 AN: 111432 Hom.: 7474 Cov.: 23 AF XY: 0.381 AC XY: 12819 AN XY: 33670

African (AFR) AF: 0.651 AC: 19911 AN: 30564

American (AMR) AF: 0.302 AC: 3179 AN: 10512

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1338 AN: 2643

East Asian (EAS) AF: 0.197 AC: 704 AN: 3565

South Asian (SAS) AF: 0.236 AC: 644 AN: 2732

European-Finnish (FIN) AF: 0.232 AC: 1399 AN: 6026

Middle Eastern (MID) AF: 0.567 AC: 122 AN: 215

European-Non Finnish (NFE) AF: 0.307 AC: 16289 AN: 52987

Other (OTH) AF: 0.423 AC: 642 AN: 1518

Alfa AF: 0.368 Hom.: 4045

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.53
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7878993; hg19: chrX-70400393;