rs4787427

Variant names:

• chr16-27375073-C-G
• rs4787427
• ENST00000722344.1:n.76+739C>G

Variant summary

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

The ENST00000722344.1(ENSG00000294275):​n.76+739C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,084 control chromosomes in the GnomAD database, including 44,521 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 0.76 (44521 hom., cov: 31)
• Consequence: ENSG00000294275 ENST00000722344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 4 publications found

Genes affected

ENSG00000294275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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
ENSG00000294275	ENST00000722344.1	n.76+739C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114922 AN: 151966 Hom.: 44449 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.757 AC: 115059 AN: 152084 Hom.: 44521 Cov.: 31 AF XY: 0.755 AC XY: 56126 AN XY: 74314

African (AFR) AF: 0.927 AC: 38492 AN: 41516

American (AMR) AF: 0.768 AC: 11741 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1860 AN: 3464

East Asian (EAS) AF: 0.694 AC: 3591 AN: 5172

South Asian (SAS) AF: 0.677 AC: 3260 AN: 4816

European-Finnish (FIN) AF: 0.689 AC: 7271 AN: 10554

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46477 AN: 67958

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.733 Hom.: 5156

Bravo AF: 0.769

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4787427; hg19: chr16-27386394;