rs1021570

Variant names:

• chrX-79716516-T-C
• rs1021570

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.23 (2333 hom., 6019 hem., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.354 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: 0.230 AC: 24236 AN: 105339 Hom.: 2330 Cov.: 19

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0986

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.230 AC: 24241 AN: 105348 Hom.: 2333 Cov.: 19 AF XY: 0.214 AC XY: 6019 AN XY: 28136

African (AFR) AF: 0.267 AC: 7776 AN: 29122

American (AMR) AF: 0.364 AC: 3479 AN: 9549

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 473 AN: 2585

East Asian (EAS) AF: 0.229 AC: 765 AN: 3340

South Asian (SAS) AF: 0.107 AC: 256 AN: 2390

European-Finnish (FIN) AF: 0.182 AC: 895 AN: 4920

Middle Eastern (MID) AF: 0.141 AC: 28 AN: 199

European-Non Finnish (NFE) AF: 0.199 AC: 10193 AN: 51147

Other (OTH) AF: 0.216 AC: 311 AN: 1437

Alfa AF: 0.231 Hom.: 1646

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.70
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1021570; hg19: chrX-78972013;