rs6644571

Variant names:

• chrX-736014-T-C
• rs6644571

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 0.464 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
• Publications: 0 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70448 AN: 151798 Hom.: 16614 Cov.: 32

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

African (AFR) AF: 0.519 AC: 21526 AN: 41456

American (AMR) AF: 0.438 AC: 6693 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1270 AN: 3464

East Asian (EAS) AF: 0.524 AC: 2711 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2034 AN: 4802

European-Finnish (FIN) AF: 0.515 AC: 5409 AN: 10510

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29500 AN: 67922

Other (OTH) AF: 0.449 AC: 948 AN: 2112

Bravo AF: 0.462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6644571; hg19: chrX-696749;