rs2897404

Variant names:

• chrX-10380285-C-T
• rs2897404

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 0.325 in 111,267 control chromosomes in the GnomAD database, including 4,558 homozygotes. There are 11,210 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 0.32 (4558 hom., 11210 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.325 AC: 36159 AN: 111212 Hom.: 4560 Cov.: 24

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.325 AC: 36160 AN: 111267 Hom.: 4558 Cov.: 24 AF XY: 0.334 AC XY: 11210 AN XY: 33583

African (AFR) AF: 0.209 AC: 6438 AN: 30768

American (AMR) AF: 0.515 AC: 5417 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1000 AN: 2635

East Asian (EAS) AF: 0.711 AC: 2515 AN: 3536

South Asian (SAS) AF: 0.340 AC: 919 AN: 2701

European-Finnish (FIN) AF: 0.351 AC: 2086 AN: 5941

Middle Eastern (MID) AF: 0.344 AC: 74 AN: 215

European-Non Finnish (NFE) AF: 0.320 AC: 16900 AN: 52756

Other (OTH) AF: 0.342 AC: 518 AN: 1514

Alfa AF: 0.315 Hom.: 2234

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs2897404; hg19: chrX-10348325;