5-176713451-T-C

Variant names:

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

Variant summary

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

The ENST00000846731.1(ENSG00000310042):​n.536+8T>C variant causes a splice region, 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: ENSG00000310042 ENST00000846731.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 1 publications found

Genes affected

ENSG00000248484 (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 (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846731.1. 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
	ENSG00000248484	ENST00000507236.1	TSL:4	n.220-5737A>G		intron	N/A
	ENSG00000310042	ENST00000846731.1		n.536+8T>C		splice_region intron	N/A
	ENSG00000310042	ENST00000846732.1		n.743+8T>C		splice_region intron	N/A

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

African (AFR) AF: 0.847 AC: 35166 AN: 41528

American (AMR) AF: 0.862 AC: 13182 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4708 AN: 5170

South Asian (SAS) AF: 0.844 AC: 4064 AN: 4814

European-Finnish (FIN) AF: 0.893 AC: 9474 AN: 10604

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60713 AN: 68006

Other (OTH) AF: 0.862 AC: 1821 AN: 2112

Alfa AF: 0.881 Hom.: 91410

Bravo AF: 0.869

Asia WGS AF: 0.861 AC: 2991 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	5.0
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2220368; hg19: chr5-176140452;