rs3027409

Variant names:

• chrX-43747786-T-G
• rs3027409

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 0.0971 in 111,167 control chromosomes in the GnomAD database, including 761 homozygotes. There are 2,825 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 0.097 (761 hom., 2825 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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: 0.0969 AC: 10772 AN: 111112 Hom.: 760 Cov.: 22

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.000282

Gnomad SAS AF: 0.0206

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0879

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0971 AC: 10799 AN: 111167 Hom.: 761 Cov.: 22 AF XY: 0.0846 AC XY: 2825 AN XY: 33401

African (AFR) AF: 0.251 AC: 7618 AN: 30368

American (AMR) AF: 0.0535 AC: 562 AN: 10496

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 191 AN: 2631

East Asian (EAS) AF: 0.000283 AC: 1 AN: 3530

South Asian (SAS) AF: 0.0206 AC: 54 AN: 2622

European-Finnish (FIN) AF: 0.0135 AC: 82 AN: 6054

Middle Eastern (MID) AF: 0.0917 AC: 20 AN: 218

European-Non Finnish (NFE) AF: 0.0404 AC: 2141 AN: 53052

Other (OTH) AF: 0.0815 AC: 123 AN: 1509

Alfa AF: 0.0635 Hom.: 7077

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.67
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs3027409; hg19: chrX-43607033;