rs10521884

Variant names:

• chrX-149461305-G-A
• rs10521884
• ENST00000836698.1:n.356G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-149461305-G-A
• chrX-149461305-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000836698.1(ENSG00000308827):​n.356G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.81 (27364 hom., 26199 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000308827 ENST00000836698.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 0 publications found

Genes affected

ENSG00000308827 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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
ENSG00000308827	ENST00000836698.1	n.356G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.809 AC: 88925 AN: 109927 Hom.: 27374 Cov.: 22

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.945

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.814

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.809 AC: 88925 AN: 109977 Hom.: 27364 Cov.: 22 AF XY: 0.813 AC XY: 26199 AN XY: 32241

African (AFR) AF: 0.461 AC: 13883 AN: 30096

American (AMR) AF: 0.765 AC: 7852 AN: 10269

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 2619 AN: 2631

East Asian (EAS) AF: 0.794 AC: 2740 AN: 3451

South Asian (SAS) AF: 0.868 AC: 2213 AN: 2551

European-Finnish (FIN) AF: 0.986 AC: 5703 AN: 5783

Middle Eastern (MID) AF: 0.944 AC: 204 AN: 216

European-Non Finnish (NFE) AF: 0.981 AC: 51816 AN: 52800

Other (OTH) AF: 0.816 AC: 1222 AN: 1498

Alfa AF: 0.876 Hom.: 7359

Bravo AF: 0.771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.36
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs10521884; hg19: chrX-148542836;