X-859810-T-C

Variant names:

• chrX-859810-T-C
• rs35766339

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 0.0412 in 150,046 control chromosomes in the GnomAD database, including 185 homozygotes. There are 2,991 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 0.041 (185 hom., 2991 hem., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0523 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: 0.0412 AC: 6184 AN: 149936 Hom.: 186 Cov.: 26

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0367

Gnomad EAS AF: 0.000793

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0404

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

GnomAD4 genome AF: 0.0412 AC: 6180 AN: 150046 Hom.: 185 Cov.: 26 AF XY: 0.0409 AC XY: 2991 AN XY: 73176

African (AFR) AF: 0.0255 AC: 1046 AN: 40992

American (AMR) AF: 0.0321 AC: 481 AN: 14976

Ashkenazi Jewish (ASJ) AF: 0.0367 AC: 127 AN: 3464

East Asian (EAS) AF: 0.000794 AC: 4 AN: 5036

South Asian (SAS) AF: 0.0459 AC: 216 AN: 4702

European-Finnish (FIN) AF: 0.0532 AC: 535 AN: 10060

Middle Eastern (MID) AF: 0.0241 AC: 7 AN: 290

European-Non Finnish (NFE) AF: 0.0537 AC: 3630 AN: 67540

Other (OTH) AF: 0.0400 AC: 83 AN: 2076

Bravo AF: 0.0390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.43
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs35766339; hg19: chrX-820545;