rs2721998

Positions:

• chrX-51608675-A-C
• chrX-51608675-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00485 in 111,562 control chromosomes in the GnomAD database, including 4 homozygotes. There are 153 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 0.0048 (4 hom., 153 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00487 AC: 543 AN: 111509 Hom.: 4 Cov.: 22 AF XY: 0.00457 AC XY: 154 AN XY: 33697

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00382

Gnomad ASJ AF: 0.00303

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00534

Gnomad FIN AF: 0.00265

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00776

Gnomad OTH AF: 0.00602

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

GnomAD4 genome AF: 0.00485 AC: 541 AN: 111562 Hom.: 4 Cov.: 22 AF XY: 0.00453 AC XY: 153 AN XY: 33760

Gnomad4 AFR AF: 0.00104

Gnomad4 AMR AF: 0.00382

Gnomad4 ASJ AF: 0.00303

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.00265

Gnomad4 NFE AF: 0.00776

Gnomad4 OTH AF: 0.00594

Alfa AF: 0.00208 Hom.: 9

Bravo AF: 0.00488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2721998; hg19: chrX-51351527;