chrX-861504-G-A

Variant names:

• chrX-861504-G-A
• rs6644384

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 0.42 in 149,068 control chromosomes in the GnomAD database, including 17,250 homozygotes. There are 31,174 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 0.42 (17250 hom., 31174 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.420 AC: 62560 AN: 148950 Hom.: 17235 Cov.: 30

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.420 AC: 62597 AN: 149068 Hom.: 17250 Cov.: 30 AF XY: 0.429 AC XY: 31174 AN XY: 72600

African (AFR) AF: 0.194 AC: 7963 AN: 41046

American (AMR) AF: 0.473 AC: 7033 AN: 14870

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1611 AN: 3432

East Asian (EAS) AF: 0.945 AC: 4873 AN: 5154

South Asian (SAS) AF: 0.710 AC: 3328 AN: 4690

European-Finnish (FIN) AF: 0.508 AC: 5153 AN: 10152

Middle Eastern (MID) AF: 0.406 AC: 117 AN: 288

European-Non Finnish (NFE) AF: 0.469 AC: 31197 AN: 66518

Other (OTH) AF: 0.459 AC: 944 AN: 2056

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6644384; hg19: chrX-822239;