chrX-66043946-G-A

Variant names:

• chrX-66043946-G-A
• rs1977106

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 0.0575 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 6394 AN: 111104 Hom.: 230 Cov.: 22

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

African (AFR) AF: 0.0124 AC: 379 AN: 30634

American (AMR) AF: 0.0265 AC: 276 AN: 10419

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 69 AN: 2638

East Asian (EAS) AF: 0.000279 AC: 1 AN: 3579

South Asian (SAS) AF: 0.0202 AC: 53 AN: 2629

European-Finnish (FIN) AF: 0.0579 AC: 344 AN: 5946

Middle Eastern (MID) AF: 0.0415 AC: 9 AN: 217

European-Non Finnish (NFE) AF: 0.0964 AC: 5102 AN: 52901

Other (OTH) AF: 0.0415 AC: 63 AN: 1518

Alfa AF: 0.0790 Hom.: 4816

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1977106; hg19: chrX-65263788;