2-215451764-C-T

Variant names:

• chr2-215451764-C-T
• rs1250255
• ENST00000767720.1:n.283+364C>T

Variant summary

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

The ENST00000767720.1(ENSG00000299965):​n.283+364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,250 control chromosomes in the GnomAD database, including 51,879 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 0.82 (51879 hom., cov: 33)
• Consequence: ENSG00000299965 ENST00000767720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 5 publications found

Genes affected

ENSG00000299965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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
ENSG00000299965	ENST00000767720.1	n.283+364C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124543 AN: 152132 Hom.: 51837 Cov.: 33

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.819 AC: 124638 AN: 152250 Hom.: 51879 Cov.: 33 AF XY: 0.818 AC XY: 60844 AN XY: 74418

African (AFR) AF: 0.948 AC: 39407 AN: 41574

American (AMR) AF: 0.787 AC: 12034 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2470 AN: 3468

East Asian (EAS) AF: 0.927 AC: 4808 AN: 5186

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4818

European-Finnish (FIN) AF: 0.817 AC: 8657 AN: 10592

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52136 AN: 68000

Other (OTH) AF: 0.796 AC: 1682 AN: 2114

Alfa AF: 0.772 Hom.: 73690

Bravo AF: 0.831

Asia WGS AF: 0.696 AC: 2417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.31
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1250255; hg19: chr2-216316487;