X-98411382-T-C

Variant names:

• chrX-98411382-T-C
• rs2105183

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 0.311 in 109,947 control chromosomes in the GnomAD database, including 4,227 homozygotes. There are 10,140 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 0.31 (4227 hom., 10140 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.311 AC: 34214 AN: 109893 Hom.: 4237 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.311 AC: 34215 AN: 109947 Hom.: 4227 Cov.: 22 AF XY: 0.314 AC XY: 10140 AN XY: 32313

African (AFR) AF: 0.218 AC: 6615 AN: 30333

American (AMR) AF: 0.479 AC: 4882 AN: 10198

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 949 AN: 2620

East Asian (EAS) AF: 0.753 AC: 2586 AN: 3433

South Asian (SAS) AF: 0.530 AC: 1355 AN: 2557

European-Finnish (FIN) AF: 0.217 AC: 1259 AN: 5798

Middle Eastern (MID) AF: 0.324 AC: 70 AN: 216

European-Non Finnish (NFE) AF: 0.301 AC: 15851 AN: 52609

Other (OTH) AF: 0.352 AC: 528 AN: 1500

Alfa AF: 0.329 Hom.: 6328

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.024
DANN	Benign	0.42
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2105183; hg19: chrX-97666380;