rs7061408

Variant names:

• chrX-82932685-G-A
• rs7061408

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 0.333 in 111,450 control chromosomes in the GnomAD database, including 5,554 homozygotes. There are 10,824 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 0.33 (5554 hom., 10824 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.333 AC: 37119 AN: 111400 Hom.: 5554 Cov.: 23

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.333 AC: 37147 AN: 111450 Hom.: 5554 Cov.: 23 AF XY: 0.321 AC XY: 10824 AN XY: 33694

African (AFR) AF: 0.585 AC: 17859 AN: 30528

American (AMR) AF: 0.334 AC: 3557 AN: 10637

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 542 AN: 2641

East Asian (EAS) AF: 0.101 AC: 355 AN: 3512

South Asian (SAS) AF: 0.254 AC: 673 AN: 2651

European-Finnish (FIN) AF: 0.216 AC: 1310 AN: 6055

Middle Eastern (MID) AF: 0.252 AC: 54 AN: 214

European-Non Finnish (NFE) AF: 0.230 AC: 12215 AN: 53014

Other (OTH) AF: 0.285 AC: 433 AN: 1517

Alfa AF: 0.294 Hom.: 1881

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7061408; hg19: chrX-82187693;