rs2178490

Variant names:

• chr5-30839224-A-G
• rs2178490
• ENST00000797583.1:n.368+35951T>C

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.368+35951T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,942 control chromosomes in the GnomAD database, including 7,117 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 0.28 (7117 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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.368+35951T>C		intron_variant	Intron 4 of 4
ENSG00000303861	ENST00000797584.1	n.276+35951T>C		intron_variant	Intron 1 of 2
ENSG00000303861	ENST00000797585.1	n.183+10766T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43227 AN: 151824 Hom.: 7089 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.285 AC: 43294 AN: 151942 Hom.: 7117 Cov.: 32 AF XY: 0.287 AC XY: 21336 AN XY: 74254

African (AFR) AF: 0.372 AC: 15420 AN: 41426

American (AMR) AF: 0.327 AC: 4990 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3444 AN: 5128

South Asian (SAS) AF: 0.394 AC: 1902 AN: 4824

European-Finnish (FIN) AF: 0.168 AC: 1779 AN: 10564

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14052 AN: 67950

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.242 Hom.: 19383

Bravo AF: 0.303

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0010
DANN	Benign	0.59
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2178490; hg19: chr5-30839331;