ENST00000690965.2:n.440+5117T>C

Variant names:

• chr3-12226148-A-G
• rs7616006
• ENST00000690965.2:n.440+5117T>C

Variant summary

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

The ENST00000690965.2(ENSG00000288952):​n.440+5117T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,054 control chromosomes in the GnomAD database, including 18,245 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 0.47 (18245 hom., cov: 32)
• Consequence: ENSG00000288952 ENST00000690965.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 33 publications found

Genes affected

ENSG00000288952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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
ENSG00000288952	ENST00000690965.2	n.440+5117T>C		intron_variant	Intron 2 of 3
ENSG00000288952	ENST00000764008.1	n.443+5117T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71883 AN: 151936 Hom.: 18214 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.473 AC: 71959 AN: 152054 Hom.: 18245 Cov.: 32 AF XY: 0.467 AC XY: 34712 AN XY: 74308

African (AFR) AF: 0.652 AC: 27041 AN: 41470

American (AMR) AF: 0.364 AC: 5563 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1510 AN: 5156

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4021 AN: 10572

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28831 AN: 67970

Other (OTH) AF: 0.486 AC: 1027 AN: 2112

Alfa AF: 0.431 Hom.: 14636

Bravo AF: 0.486

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.55
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7616006; hg19: chr3-12267648;