rs1229078

Variant names:

• chrX-16203781-T-A
• rs1229078

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 0.398 in 110,660 control chromosomes in the GnomAD database, including 6,987 homozygotes. There are 12,334 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 0.40 (6987 hom., 12334 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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: 0.398 AC: 43977 AN: 110610 Hom.: 6988 Cov.: 22

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.398 AC: 44002 AN: 110660 Hom.: 6987 Cov.: 22 AF XY: 0.374 AC XY: 12334 AN XY: 32954

African (AFR) AF: 0.551 AC: 16748 AN: 30403

American (AMR) AF: 0.387 AC: 4032 AN: 10406

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 937 AN: 2629

East Asian (EAS) AF: 0.111 AC: 393 AN: 3544

South Asian (SAS) AF: 0.274 AC: 717 AN: 2614

European-Finnish (FIN) AF: 0.236 AC: 1389 AN: 5876

Middle Eastern (MID) AF: 0.389 AC: 82 AN: 211

European-Non Finnish (NFE) AF: 0.357 AC: 18839 AN: 52809

Other (OTH) AF: 0.369 AC: 553 AN: 1497

Alfa AF: 0.374 Hom.: 2488

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1229078; hg19: chrX-16221904;