rs17340307

Variant names:

• chrX-103328938-T-G
• rs17340307

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 0.0127 in 112,391 control chromosomes in the GnomAD database, including 67 homozygotes. There are 468 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 0.013 (67 hom., 468 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.0127 AC: 1424 AN: 112337 Hom.: 65 Cov.: 23

Gnomad AFR AF: 0.00385

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.00922

Gnomad FIN AF: 0.00456

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000994

Gnomad OTH AF: 0.0159

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

GnomAD4 genome AF: 0.0127 AC: 1427 AN: 112391 Hom.: 67 Cov.: 23 AF XY: 0.0135 AC XY: 468 AN XY: 34553

African (AFR) AF: 0.00384 AC: 119 AN: 30996

American (AMR) AF: 0.0433 AC: 460 AN: 10619

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2659

East Asian (EAS) AF: 0.201 AC: 710 AN: 3530

South Asian (SAS) AF: 0.0104 AC: 28 AN: 2703

European-Finnish (FIN) AF: 0.00456 AC: 28 AN: 6139

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.000975 AC: 52 AN: 53313

Other (OTH) AF: 0.0196 AC: 30 AN: 1529

Alfa AF: 0.00842 Hom.: 41

Bravo AF: 0.0195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs17340307; hg19: chrX-102583866;