5-30936683-C-T

Variant names:

• chr5-30936683-C-T
• rs17667845
• ENST00000797583.1:n.122-31097G>A

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.122-31097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,954 control chromosomes in the GnomAD database, including 7,661 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 0.31 (7661 hom., cov: 33)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797583.1. 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
	ENSG00000303861	ENST00000797583.1		n.122-31097G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46518 AN: 151834 Hom.: 7658 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.306 AC: 46521 AN: 151954 Hom.: 7661 Cov.: 33 AF XY: 0.307 AC XY: 22811 AN XY: 74258

African (AFR) AF: 0.191 AC: 7914 AN: 41478

American (AMR) AF: 0.306 AC: 4657 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1266 AN: 5164

South Asian (SAS) AF: 0.301 AC: 1452 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4080 AN: 10576

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24750 AN: 67896

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.228 Hom.: 560

Bravo AF: 0.293

Asia WGS AF: 0.271 AC: 938 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.65
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs17667845; hg19: chr5-30936790;