rs7049377

Variant names:

• chrX-100880499-G-A
• rs7049377

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.234 in 110,644 control chromosomes in the GnomAD database, including 2,242 homozygotes. There are 7,690 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 (2242 hom., 7690 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 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: 0.234 AC: 25889 AN: 110590 Hom.: 2247 Cov.: 23 AF XY: 0.234 AC XY: 7681 AN XY: 32842

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.234 AC: 25884 AN: 110644 Hom.: 2242 Cov.: 23 AF XY: 0.234 AC XY: 7690 AN XY: 32906

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.254

Alfa AF: 0.235 Hom.: 19197

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7049377; hg19: chrX-100135488;