rs6644571

Positions:

• chrX-736014-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.464 in 151,916 control chromosomes in the GnomAD database, including 16,646 homozygotes. There are 34,724 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 0.46 (16646 hom., 34724 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70448 AN: 151798 Hom.: 16614 Cov.: 32 AF XY: 0.468 AC XY: 34647 AN XY: 74078

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.464 AC: 70531 AN: 151916 Hom.: 16646 Cov.: 32 AF XY: 0.468 AC XY: 34724 AN XY: 74206

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.449

Bravo AF: 0.462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6644571; hg19: chrX-696749;