rs17312728

Variant names:

• chrX-147727801-A-C
• rs17312728

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 0.178 in 110,109 control chromosomes in the GnomAD database, including 1,457 homozygotes. There are 5,403 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 0.18 (1457 hom., 5403 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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: 0.178 AC: 19645 AN: 110064 Hom.: 1456 Cov.: 22

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.178 AC: 19644 AN: 110109 Hom.: 1457 Cov.: 22 AF XY: 0.167 AC XY: 5403 AN XY: 32431

African (AFR) AF: 0.165 AC: 5001 AN: 30275

American (AMR) AF: 0.111 AC: 1155 AN: 10367

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 414 AN: 2615

East Asian (EAS) AF: 0.00599 AC: 21 AN: 3506

South Asian (SAS) AF: 0.0694 AC: 178 AN: 2566

European-Finnish (FIN) AF: 0.217 AC: 1249 AN: 5759

Middle Eastern (MID) AF: 0.245 AC: 52 AN: 212

European-Non Finnish (NFE) AF: 0.213 AC: 11216 AN: 52631

Other (OTH) AF: 0.176 AC: 265 AN: 1502

Alfa AF: 0.196 Hom.: 1164

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs17312728; hg19: chrX-146809319;