chrX-144281548-C-T

Variant names:

• chrX-144281548-C-T
• rs6637197

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 0.191 in 111,609 control chromosomes in the GnomAD database, including 1,574 homozygotes. There are 6,316 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 0.19 (1574 hom., 6316 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.191 AC: 21323 AN: 111555 Hom.: 1573 Cov.: 22

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.191 AC: 21339 AN: 111609 Hom.: 1574 Cov.: 22 AF XY: 0.187 AC XY: 6316 AN XY: 33843

African (AFR) AF: 0.206 AC: 6324 AN: 30706

American (AMR) AF: 0.314 AC: 3323 AN: 10576

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 621 AN: 2642

East Asian (EAS) AF: 0.267 AC: 935 AN: 3499

South Asian (SAS) AF: 0.171 AC: 466 AN: 2725

European-Finnish (FIN) AF: 0.144 AC: 861 AN: 5988

Middle Eastern (MID) AF: 0.294 AC: 62 AN: 211

European-Non Finnish (NFE) AF: 0.154 AC: 8186 AN: 53064

Other (OTH) AF: 0.247 AC: 375 AN: 1518

Alfa AF: 0.175 Hom.: 13180

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6637197; hg19: chrX-143364654;