rs1029496

Variant names:

• chrX-24379974-A-G
• rs1029496
• ENST00000737420.1:n.306+2022A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000737420.1(ENSG00000296219):​n.306+2022A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 112,614 control chromosomes in the GnomAD database, including 649 homozygotes. There are 4,390 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 0.12 (649 hom., 4390 hem., cov: 24)
• Consequence: ENSG00000296219 ENST00000737420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 1 publications found

Genes affected

ENSG00000296219 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.241 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
ENSG00000296219	ENST00000737420.1	n.306+2022A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 13695 AN: 112559 Hom.: 648 Cov.: 24

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.0392

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.122 AC: 13696 AN: 112614 Hom.: 649 Cov.: 24 AF XY: 0.126 AC XY: 4390 AN XY: 34784

African (AFR) AF: 0.0659 AC: 2053 AN: 31143

American (AMR) AF: 0.162 AC: 1732 AN: 10704

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 259 AN: 2654

East Asian (EAS) AF: 0.141 AC: 504 AN: 3584

South Asian (SAS) AF: 0.257 AC: 702 AN: 2729

European-Finnish (FIN) AF: 0.207 AC: 1259 AN: 6094

Middle Eastern (MID) AF: 0.124 AC: 27 AN: 217

European-Non Finnish (NFE) AF: 0.130 AC: 6936 AN: 53253

Other (OTH) AF: 0.127 AC: 197 AN: 1548

Alfa AF: 0.111 Hom.: 2038

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.38
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1029496; hg19: chrX-24398091;