rs5913060

Variant names:

• chrX-79727276-G-A
• rs5913060

Your query was ambiguous. Multiple possible variants found:

• chrX-79727276-G-A
• chrX-79727276-G-C

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 0.232 in 108,678 control chromosomes in the GnomAD database, including 2,350 homozygotes. There are 6,903 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 0.23 (2350 hom., 6903 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.36 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: 0.232 AC: 25245 AN: 108625 Hom.: 2347 Cov.: 21

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.232 AC: 25262 AN: 108678 Hom.: 2350 Cov.: 21 AF XY: 0.222 AC XY: 6903 AN XY: 31108

African (AFR) AF: 0.265 AC: 7913 AN: 29811

American (AMR) AF: 0.370 AC: 3750 AN: 10139

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 485 AN: 2617

East Asian (EAS) AF: 0.242 AC: 817 AN: 3380

South Asian (SAS) AF: 0.114 AC: 283 AN: 2480

European-Finnish (FIN) AF: 0.193 AC: 1065 AN: 5505

Middle Eastern (MID) AF: 0.153 AC: 33 AN: 216

European-Non Finnish (NFE) AF: 0.201 AC: 10519 AN: 52384

Other (OTH) AF: 0.222 AC: 327 AN: 1474

Alfa AF: 0.108 Hom.: 551

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.24
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs5913060; hg19: chrX-78982773;