ENST00000816576.1:n.315-16599C>T

Variant names:

• chr4-161225960-G-A
• rs719880
• ENST00000816576.1:n.315-16599C>T

Variant summary

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

The ENST00000816576.1(ENSG00000306264):​n.315-16599C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,948 control chromosomes in the GnomAD database, including 8,564 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 0.32 (8564 hom., cov: 32)
• Consequence: ENSG00000306264 ENST00000816576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 3 publications found

Genes affected

ENSG00000306264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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
ENSG00000306264	ENST00000816576.1	n.315-16599C>T		intron_variant	Intron 2 of 3
ENSG00000306264	ENST00000816577.1	n.313+16980C>T		intron_variant	Intron 2 of 2
ENSG00000306264	ENST00000816578.1	n.339+16980C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48730 AN: 151828 Hom.: 8561 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.321 AC: 48731 AN: 151948 Hom.: 8564 Cov.: 32 AF XY: 0.316 AC XY: 23495 AN XY: 74272

African (AFR) AF: 0.241 AC: 9985 AN: 41444

American (AMR) AF: 0.273 AC: 4173 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.0599 AC: 310 AN: 5178

South Asian (SAS) AF: 0.183 AC: 882 AN: 4824

European-Finnish (FIN) AF: 0.430 AC: 4514 AN: 10500

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26494 AN: 67940

Other (OTH) AF: 0.333 AC: 704 AN: 2114

Alfa AF: 0.368 Hom.: 16531

Bravo AF: 0.307

Asia WGS AF: 0.131 AC: 455 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs719880; hg19: chr4-162147112;