rs7066438

Variant names:

• chrX-71179969-A-T
• rs7066438
• ENST00000740246.1:n.346+3942T>A

Variant summary

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

The ENST00000740246.1(ENSG00000228427):​n.346+3942T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 109,985 control chromosomes in the GnomAD database, including 7,954 homozygotes. There are 12,385 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 0.41 (7954 hom., 12385 hem., cov: 22)
• Consequence: ENSG00000228427 ENST00000740246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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+3942T>A		intron_variant	Intron 2 of 4
ENSG00000228427	ENST00000740247.1	n.367+3942T>A		intron_variant	Intron 2 of 3
ENSG00000228427	ENST00000740248.1	n.310+1306T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 44734 AN: 109931 Hom.: 7951 Cov.: 22

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.550

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.407 AC: 44780 AN: 109985 Hom.: 7954 Cov.: 22 AF XY: 0.383 AC XY: 12385 AN XY: 32339

African (AFR) AF: 0.681 AC: 20422 AN: 29996

American (AMR) AF: 0.303 AC: 3131 AN: 10327

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1325 AN: 2620

East Asian (EAS) AF: 0.197 AC: 693 AN: 3510

South Asian (SAS) AF: 0.220 AC: 569 AN: 2586

European-Finnish (FIN) AF: 0.225 AC: 1320 AN: 5854

Middle Eastern (MID) AF: 0.571 AC: 124 AN: 217

European-Non Finnish (NFE) AF: 0.309 AC: 16283 AN: 52707

Other (OTH) AF: 0.429 AC: 645 AN: 1502

Alfa AF: 0.368 Hom.: 2519

Bravo AF: 0.428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.88
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7066438; hg19: chrX-70399819;