chrX-144939673-T-C

Variant names:

• chrX-144939673-T-C
• rs17410

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 0.478 in 111,420 control chromosomes in the GnomAD database, including 9,360 homozygotes. There are 15,732 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 0.48 (9360 hom., 15732 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.478 AC: 53190 AN: 111367 Hom.: 9356 Cov.: 24

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.478 AC: 53246 AN: 111420 Hom.: 9360 Cov.: 24 AF XY: 0.467 AC XY: 15732 AN XY: 33676

African (AFR) AF: 0.618 AC: 18973 AN: 30681

American (AMR) AF: 0.479 AC: 5106 AN: 10657

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1031 AN: 2631

East Asian (EAS) AF: 0.338 AC: 1176 AN: 3480

South Asian (SAS) AF: 0.373 AC: 995 AN: 2669

European-Finnish (FIN) AF: 0.444 AC: 2691 AN: 6065

Middle Eastern (MID) AF: 0.306 AC: 66 AN: 216

European-Non Finnish (NFE) AF: 0.423 AC: 22329 AN: 52818

Other (OTH) AF: 0.493 AC: 753 AN: 1528

Alfa AF: 0.464 Hom.: 3648

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs17410; hg19: chrX-144021193;