X-79717665-G-C

Variant names:

• chrX-79717665-G-C
• rs17003827

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 0.243 in 105,163 control chromosomes in the GnomAD database, including 2,353 homozygotes. There are 7,160 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 0.24 (2353 hom., 7160 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 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: 0.243 AC: 25509 AN: 105117 Hom.: 2350 Cov.: 21

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.243 AC: 25524 AN: 105163 Hom.: 2353 Cov.: 21 AF XY: 0.258 AC XY: 7160 AN XY: 27771

African (AFR) AF: 0.270 AC: 7984 AN: 29590

American (AMR) AF: 0.398 AC: 3814 AN: 9580

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 491 AN: 2534

East Asian (EAS) AF: 0.241 AC: 826 AN: 3429

South Asian (SAS) AF: 0.130 AC: 290 AN: 2237

European-Finnish (FIN) AF: 0.224 AC: 1093 AN: 4883

Middle Eastern (MID) AF: 0.164 AC: 34 AN: 207

European-Non Finnish (NFE) AF: 0.209 AC: 10582 AN: 50635

Other (OTH) AF: 0.242 AC: 342 AN: 1415

Alfa AF: 0.113 Hom.: 557

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs17003827; hg19: chrX-78973162;