4-33685038-G-C

Variant names:

• chr4-33685038-G-C
• rs719776
• ENST00000673514.1:n.1365-8319G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673514.1(ENSG00000288321):​n.1365-8319G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,800 control chromosomes in the GnomAD database, including 15,744 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 0.33 (15744 hom., cov: 32)
• Consequence: ENSG00000288321 ENST00000673514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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
ENSG00000288321	ENST00000673514.1	n.1365-8319G>C		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49979 AN: 151682 Hom.: 15691 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.330 AC: 50089 AN: 151800 Hom.: 15744 Cov.: 32 AF XY: 0.328 AC XY: 24323 AN XY: 74162

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.281

Alfa AF: 0.0639 Hom.: 95

Bravo AF: 0.361

Asia WGS AF: 0.322 AC: 1119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719776; hg19: chr4-33686660;