rs1392421

Variant names:

• chr5-30935291-G-A
• rs1392421
• ENST00000797583.1:n.122-29705C>T

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.122-29705C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,804 control chromosomes in the GnomAD database, including 7,037 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 0.29 (7037 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.924
• Publications: 0 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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
ENSG00000303861	ENST00000797583.1	n.122-29705C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44596 AN: 151688 Hom.: 7033 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.294 AC: 44603 AN: 151804 Hom.: 7037 Cov.: 32 AF XY: 0.294 AC XY: 21829 AN XY: 74160

African (AFR) AF: 0.188 AC: 7786 AN: 41432

American (AMR) AF: 0.296 AC: 4510 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1248 AN: 5132

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4814

European-Finnish (FIN) AF: 0.374 AC: 3931 AN: 10502

Middle Eastern (MID) AF: 0.334 AC: 97 AN: 290

European-Non Finnish (NFE) AF: 0.347 AC: 23587 AN: 67900

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.319 Hom.: 19541

Bravo AF: 0.282

Asia WGS AF: 0.255 AC: 886 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.55
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1392421; hg19: chr5-30935398;