rs7881412

Variant names:

• chrX-6251419-G-A
• rs7881412

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 0.112 in 111,342 control chromosomes in the GnomAD database, including 694 homozygotes. There are 3,502 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 0.11 (694 hom., 3502 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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: 0.112 AC: 12478 AN: 111291 Hom.: 694 Cov.: 23

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.0890

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.112 AC: 12480 AN: 111342 Hom.: 694 Cov.: 23 AF XY: 0.104 AC XY: 3502 AN XY: 33586

African (AFR) AF: 0.208 AC: 6364 AN: 30561

American (AMR) AF: 0.0590 AC: 618 AN: 10469

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 284 AN: 2653

East Asian (EAS) AF: 0.00168 AC: 6 AN: 3569

South Asian (SAS) AF: 0.0873 AC: 232 AN: 2657

European-Finnish (FIN) AF: 0.0693 AC: 413 AN: 5956

Middle Eastern (MID) AF: 0.0930 AC: 20 AN: 215

European-Non Finnish (NFE) AF: 0.0797 AC: 4232 AN: 53066

Other (OTH) AF: 0.0922 AC: 140 AN: 1519

Alfa AF: 0.0859 Hom.: 1596

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.75
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs7881412; hg19: chrX-6169460;