rs886605

Variant names:

• chrX-117247696-T-C
• rs886605

Variant summary

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

The variant allele was found at a frequency of 0.458 in 111,355 control chromosomes in the GnomAD database, including 8,610 homozygotes. There are 15,124 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 0.46 (8610 hom., 15124 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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

Frequencies

GnomAD3 genomes AF: 0.458 AC: 50956 AN: 111301 Hom.: 8615 Cov.: 24

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.457

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.458 AC: 50967 AN: 111355 Hom.: 8610 Cov.: 24 AF XY: 0.449 AC XY: 15124 AN XY: 33661

African (AFR) AF: 0.353 AC: 10845 AN: 30702

American (AMR) AF: 0.362 AC: 3828 AN: 10580

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1339 AN: 2630

East Asian (EAS) AF: 0.261 AC: 914 AN: 3501

South Asian (SAS) AF: 0.355 AC: 958 AN: 2702

European-Finnish (FIN) AF: 0.519 AC: 3092 AN: 5955

Middle Eastern (MID) AF: 0.455 AC: 96 AN: 211

European-Non Finnish (NFE) AF: 0.544 AC: 28759 AN: 52890

Other (OTH) AF: 0.445 AC: 672 AN: 1511

Alfa AF: 0.510 Hom.: 3688

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.48
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs886605; hg19: chrX-116381659;