X-71179599-TC-TCC

Variant names:

• chrX-71179599-T-TC
• rs11399763
• ENST00000740246.1:n.346+4311_346+4312insG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000740246.1(ENSG00000228427):​n.346+4311_346+4312insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (7848 hom., 12298 hem., cov: 0)
• Consequence: ENSG00000228427 ENST00000740246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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+4311_346+4312insG		intron_variant	Intron 2 of 4
ENSG00000228427	ENST00000740247.1	n.367+4311_367+4312insG		intron_variant	Intron 2 of 3
ENSG00000228427	ENST00000740248.1	n.310+1675_310+1676insG		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 44288 AN: 110082 Hom.: 7844 Cov.: 0

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.536

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.403 AC: 44334 AN: 110134 Hom.: 7848 Cov.: 0 AF XY: 0.379 AC XY: 12298 AN XY: 32456

African (AFR) AF: 0.680 AC: 20408 AN: 30033

American (AMR) AF: 0.303 AC: 3138 AN: 10370

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1336 AN: 2626

East Asian (EAS) AF: 0.196 AC: 693 AN: 3528

South Asian (SAS) AF: 0.209 AC: 553 AN: 2640

European-Finnish (FIN) AF: 0.225 AC: 1320 AN: 5868

Middle Eastern (MID) AF: 0.565 AC: 122 AN: 216

European-Non Finnish (NFE) AF: 0.301 AC: 15860 AN: 52685

Other (OTH) AF: 0.423 AC: 634 AN: 1499

Alfa AF: 0.0991 Hom.: 398

Asia WGS AF: 0.262 AC: 663 AN: 2522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11399763; hg19: chrX-70399449;