4-4924439-G-A

Variant names:

• chr4-4924439-G-A
• rs13139027
• ENST00000774609.1:n.141+3279G>A

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.141+3279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,194 control chromosomes in the GnomAD database, including 315 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 0.063 (315 hom., cov: 32)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 3 publications found

Genes affected

ENSG00000300857 (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 (AMR) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928306	NR_125893.1	n.353+3279G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300857	ENST00000774609.1	n.141+3279G>A		intron_variant	Intron 2 of 8
ENSG00000300857	ENST00000774610.1	n.164+3279G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9508 AN: 152076 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0627 AC: 9544 AN: 152194 Hom.: 315 Cov.: 32 AF XY: 0.0606 AC XY: 4507 AN XY: 74390

African (AFR) AF: 0.0568 AC: 2359 AN: 41522

American (AMR) AF: 0.0888 AC: 1357 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5162

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4822

European-Finnish (FIN) AF: 0.0407 AC: 431 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4896 AN: 68020

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0705 Hom.: 767

Bravo AF: 0.0671

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.54
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs13139027; hg19: chr4-4926166;