ENST00000664749.1:n.288+10545T>G

Variant names:

• chr2-62579956-A-C
• rs1406002
• ENST00000664749.1:n.288+10545T>G

Variant summary

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

The ENST00000664749.1(ENSG00000226622):​n.288+10545T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,024 control chromosomes in the GnomAD database, including 29,955 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 0.62 (29955 hom., cov: 32)
• Consequence: ENSG00000226622 ENST00000664749.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

ENSG00000226622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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
ENSG00000226622	ENST00000664749.1	n.288+10545T>G		intron_variant	Intron 3 of 3
ENSG00000226622	ENST00000668814.1	n.305-1312T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94614 AN: 151906 Hom.: 29936 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.623 AC: 94684 AN: 152024 Hom.: 29955 Cov.: 32 AF XY: 0.622 AC XY: 46187 AN XY: 74306

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.614

Alfa AF: 0.547 Hom.: 14630

Bravo AF: 0.632

Asia WGS AF: 0.667 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406002; hg19: chr2-62807091;