rs7064448

Variant names:

• chrX-83274556-C-T
• rs7064448

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 0.195 in 110,175 control chromosomes in the GnomAD database, including 1,686 homozygotes. There are 6,108 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 0.19 (1686 hom., 6108 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 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: 0.195 AC: 21467 AN: 110127 Hom.: 1686 Cov.: 22

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0382

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.195 AC: 21471 AN: 110175 Hom.: 1686 Cov.: 22 AF XY: 0.188 AC XY: 6108 AN XY: 32515

African (AFR) AF: 0.278 AC: 8404 AN: 30215

American (AMR) AF: 0.286 AC: 2935 AN: 10249

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 284 AN: 2634

East Asian (EAS) AF: 0.176 AC: 609 AN: 3461

South Asian (SAS) AF: 0.132 AC: 342 AN: 2585

European-Finnish (FIN) AF: 0.170 AC: 997 AN: 5862

Middle Eastern (MID) AF: 0.194 AC: 42 AN: 216

European-Non Finnish (NFE) AF: 0.142 AC: 7510 AN: 52774

Other (OTH) AF: 0.215 AC: 322 AN: 1499

Alfa AF: 0.171 Hom.: 12566

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.62
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7064448; hg19: chrX-82529564;