rs7049502

Variant names:

• chrX-885443-G-C
• rs7049502

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 0.0857 in 152,044 control chromosomes in the GnomAD database, including 689 homozygotes. There are 6,211 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 0.086 (689 hom., 6211 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0856 AC: 13000 AN: 151926 Hom.: 679 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0902

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

GnomAD4 genome AF: 0.0857 AC: 13036 AN: 152044 Hom.: 689 Cov.: 32 AF XY: 0.0836 AC XY: 6211 AN XY: 74328

African (AFR) AF: 0.145 AC: 5993 AN: 41454

American (AMR) AF: 0.0624 AC: 954 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3468

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5172

South Asian (SAS) AF: 0.125 AC: 599 AN: 4802

European-Finnish (FIN) AF: 0.0475 AC: 503 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4504 AN: 67978

Other (OTH) AF: 0.0907 AC: 191 AN: 2106

Bravo AF: 0.0866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.063
DANN	Benign	0.12
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7049502; hg19: chrX-846178;