rs2053896

chr4-136233641-G-A

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, non coding transcript 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: ENST00000500324.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500324.2	n.363+27768C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000513332.5	n.279+27768C>T		intron_variant, non_coding_transcript_variant		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;