ENST00000670606.1:n.765-69390G>T

Variant names:

• chr2-76013235-G-T
• rs436000
• ENST00000670606.1:n.765-69390G>T

Variant summary

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

The ENST00000670606.1(ENSG00000287474):​n.765-69390G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,762 control chromosomes in the GnomAD database, including 9,127 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 0.34 (9127 hom., cov: 32)
• Consequence: ENSG00000287474 ENST00000670606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 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
ENSG00000287474	ENST00000670606.1	n.765-69390G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52003 AN: 151642 Hom.: 9116 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.343 AC: 52038 AN: 151762 Hom.: 9127 Cov.: 32 AF XY: 0.341 AC XY: 25266 AN XY: 74170

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.347

Alfa AF: 0.344 Hom.: 16620

Bravo AF: 0.344

Asia WGS AF: 0.334 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.081
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs436000; hg19: chr2-76240361;