5-176713451-T-C

Variant names:

• chr5-176713451-T-C
• rs2220368
• ENST00000507236.1:n.220-5737A>G

Variant summary

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

The ENST00000507236.1(ENSG00000248484):​n.220-5737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,210 control chromosomes in the GnomAD database, including 58,239 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 0.87 (58239 hom., cov: 31)
• Consequence: ENSG00000248484 ENST00000507236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

ENSG00000248484 (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 (EAS) allele frequency at 95% confidence interval = 0.889 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
ENSG00000248484	ENST00000507236.1	n.220-5737A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132966 AN: 152092 Hom.: 58194 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.874 AC: 133067 AN: 152210 Hom.: 58239 Cov.: 31 AF XY: 0.874 AC XY: 64993 AN XY: 74404

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.862

Alfa AF: 0.883 Hom.: 75120

Bravo AF: 0.869

Asia WGS AF: 0.861 AC: 2991 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	5.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220368; hg19: chr5-176140452;