5-180981830-C-T

Variant names:

• chr5-180981830-C-T
• rs4444930
• ENST00000766731.1:n.395-29971G>A

Variant summary

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

The ENST00000766731.1(ENSG00000299843):​n.395-29971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 134,520 control chromosomes in the GnomAD database, including 1,821 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 0.056 (1821 hom., cov: 24)
• Consequence: ENSG00000299843 ENST00000766731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598
• Publications: 3 publications found

Genes affected

ENSG00000299843 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0879 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
ENSG00000299843	ENST00000766731.1	n.395-29971G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 7550 AN: 134414 Hom.: 1822 Cov.: 24

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000439

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0561 AC: 7547 AN: 134520 Hom.: 1821 Cov.: 24 AF XY: 0.0560 AC XY: 3665 AN XY: 65434

African (AFR) AF: 0.0123 AC: 480 AN: 38958

American (AMR) AF: 0.0474 AC: 610 AN: 12866

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 128 AN: 3242

East Asian (EAS) AF: 0.000440 AC: 2 AN: 4544

South Asian (SAS) AF: 0.0466 AC: 212 AN: 4552

European-Finnish (FIN) AF: 0.0758 AC: 663 AN: 8742

Middle Eastern (MID) AF: 0.117 AC: 31 AN: 266

European-Non Finnish (NFE) AF: 0.0899 AC: 5281 AN: 58720

Other (OTH) AF: 0.0565 AC: 106 AN: 1876

Alfa AF: 0.0530 Hom.: 179

Asia WGS AF: 0.0280 AC: 94 AN: 3320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.39
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4444930; hg19: chr5-180408830;