2-76013235-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.380 AC: 15746 AN: 41416

American (AMR) AF: 0.315 AC: 4791 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3466

East Asian (EAS) AF: 0.235 AC: 1209 AN: 5142

South Asian (SAS) AF: 0.447 AC: 2150 AN: 4814

European-Finnish (FIN) AF: 0.259 AC: 2724 AN: 10530

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22647 AN: 67884

Other (OTH) AF: 0.347 AC: 726 AN: 2092

Alfa AF: 0.344 Hom.: 24765

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs436000; hg19: chr2-76240361;