rs2053896

Variant names:

• chr4-136233641-G-A
• rs2053896
• ENST00000500324.2:n.363+27768C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500324.2(ENSG00000251567):​n.363+27768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 152,018 control chromosomes in the GnomAD database, including 940 homozygotes. 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 0.096 (940 hom., cov: 32)
• Consequence: ENSG00000251567 ENST00000500324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

ENSG00000251567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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
ENSG00000251567	ENST00000500324.2	n.363+27768C>T		intron_variant	Intron 2 of 2	3
ENSG00000251567	ENST00000513332.5	n.279+27768C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14529 AN: 151900 Hom.: 940 Cov.: 32

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.0955 AC: 14518 AN: 152018 Hom.: 940 Cov.: 32 AF XY: 0.0976 AC XY: 7252 AN XY: 74320

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.100

Alfa AF: 0.115 Hom.: 1428

Bravo AF: 0.0843

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053896; hg19: chr4-137154796;