rs1392280

Variant names:

• chr5-166248678-T-C
• rs1392280
• ENST00000821541.1:n.224+3604A>G

Variant summary

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

The ENST00000821541.1(ENSG00000306847):​n.224+3604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,770 control chromosomes in the GnomAD database, including 33,011 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 0.66 (33011 hom., cov: 30)
• Consequence: ENSG00000306847 ENST00000821541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 3 publications found

Genes affected

ENSG00000306847 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821541.1. 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
	ENSG00000306847	ENST00000821541.1		n.224+3604A>G		intron	N/A
	ENSG00000306847	ENST00000821542.1		n.203+3604A>G		intron	N/A
	ENSG00000306847	ENST00000821543.1		n.171+3604A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99555 AN: 151652 Hom.: 32976 Cov.: 30

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.657 AC: 99646 AN: 151770 Hom.: 33011 Cov.: 30 AF XY: 0.653 AC XY: 48467 AN XY: 74172

African (AFR) AF: 0.723 AC: 29930 AN: 41408

American (AMR) AF: 0.533 AC: 8102 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3078 AN: 5136

South Asian (SAS) AF: 0.673 AC: 3236 AN: 4810

European-Finnish (FIN) AF: 0.663 AC: 6971 AN: 10518

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44097 AN: 67910

Other (OTH) AF: 0.610 AC: 1284 AN: 2106

Alfa AF: 0.639 Hom.: 50004

Bravo AF: 0.649

Asia WGS AF: 0.601 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1392280; hg19: chr5-165675683;