rs1977106

chrX-66043946-G-A

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 0.0575 in 111,158 control chromosomes in the GnomAD database, including 230 homozygotes. There are 1,713 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 0.058 (230 hom., 1713 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 6394 AN: 111104 Hom.: 230 Cov.: 22 AF XY: 0.0514 AC XY: 1711 AN XY: 33318

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.000279

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0422

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0575 AC: 6394 AN: 111158 Hom.: 230 Cov.: 22 AF XY: 0.0513 AC XY: 1713 AN XY: 33382

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.000279

Gnomad4 SAS AF: 0.0202

Gnomad4 FIN AF: 0.0579

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.0415

Alfa AF: 0.0827 Hom.: 3876

Bravo AF: 0.0528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1977106; hg19: chrX-65263788;