X-99197876-A-G

Variant names:

• chrX-99197876-A-G
• rs226711

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 0.276 in 106,960 control chromosomes in the GnomAD database, including 5,770 homozygotes. There are 7,746 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 0.28 (5770 hom., 7746 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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: 0.275 AC: 29431 AN: 106938 Hom.: 5765 Cov.: 21

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.276 AC: 29481 AN: 106960 Hom.: 5770 Cov.: 21 AF XY: 0.259 AC XY: 7746 AN XY: 29894

African (AFR) AF: 0.699 AC: 20525 AN: 29377

American (AMR) AF: 0.142 AC: 1409 AN: 9934

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 431 AN: 2603

East Asian (EAS) AF: 0.0922 AC: 316 AN: 3429

South Asian (SAS) AF: 0.0948 AC: 237 AN: 2499

European-Finnish (FIN) AF: 0.0889 AC: 445 AN: 5004

Middle Eastern (MID) AF: 0.199 AC: 41 AN: 206

European-Non Finnish (NFE) AF: 0.109 AC: 5650 AN: 51784

Other (OTH) AF: 0.233 AC: 339 AN: 1455

Alfa AF: 0.151 Hom.: 5104

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs226711; hg19: chrX-98452874;