5-30832796-A-G

Variant names:

• chr5-30832796-A-G
• rs10940923
• ENST00000797583.1:n.369-42137T>C

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.369-42137T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,158 control chromosomes in the GnomAD database, including 54,234 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 0.84 (54234 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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.369-42137T>C		intron_variant	Intron 4 of 4
ENSG00000303861	ENST00000797584.1	n.277-42137T>C		intron_variant	Intron 1 of 2
ENSG00000303861	ENST00000797585.1	n.183+17194T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128142 AN: 152040 Hom.: 54177 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.843 AC: 128258 AN: 152158 Hom.: 54234 Cov.: 32 AF XY: 0.843 AC XY: 62739 AN XY: 74380

African (AFR) AF: 0.877 AC: 36433 AN: 41534

American (AMR) AF: 0.847 AC: 12921 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5034 AN: 5172

South Asian (SAS) AF: 0.907 AC: 4375 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8025 AN: 10582

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55768 AN: 67990

Other (OTH) AF: 0.848 AC: 1794 AN: 2116

Alfa AF: 0.825 Hom.: 8494

Bravo AF: 0.853

Asia WGS AF: 0.940 AC: 3266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.55
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10940923; hg19: chr5-30832903;