rs2053896

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000251567 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500324.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251567	ENST00000500324.2	TSL:3	n.363+27768C>T		intron	N/A
	ENSG00000251567	ENST00000513332.5	TSL:3	n.279+27768C>T		intron	N/A
	ENSG00000251567	ENST00000835416.1		n.271+27768C>T		intron	N/A

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

African (AFR) AF: 0.0257 AC: 1065 AN: 41520

American (AMR) AF: 0.0706 AC: 1077 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1139 AN: 5152

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1435 AN: 10592

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7822 AN: 67902

Other (OTH) AF: 0.100 AC: 212 AN: 2110

Alfa AF: 0.111 Hom.: 1724

Bravo AF: 0.0843

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.46
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2053896; hg19: chr4-137154796;