rs4669887

Variant names:

• chr2-12836053-T-G
• rs4669887
• ENST00000663507.1:n.432+46106A>C

Variant summary

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

The ENST00000663507.1(ENSG00000225649):​n.432+46106A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,216 control chromosomes in the GnomAD database, including 51,523 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 (51523 hom., cov: 33)
• Consequence: ENSG00000225649 ENST00000663507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731
• Publications: 2 publications found

Genes affected

ENSG00000225649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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
ENSG00000225649	ENST00000663507.1	n.432+46106A>C		intron_variant	Intron 4 of 6
ENSG00000225649	ENST00000848763.1	n.320-49073A>C		intron_variant	Intron 3 of 4
ENSG00000225649	ENST00000848764.1	n.324+79774A>C		intron_variant	Intron 2 of 3
ENSG00000225649	ENST00000848765.1	n.166+79774A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124802 AN: 152098 Hom.: 51460 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.821 AC: 124926 AN: 152216 Hom.: 51523 Cov.: 33 AF XY: 0.822 AC XY: 61164 AN XY: 74416

African (AFR) AF: 0.875 AC: 36350 AN: 41524

American (AMR) AF: 0.799 AC: 12221 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2820 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5104 AN: 5166

South Asian (SAS) AF: 0.802 AC: 3870 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8976 AN: 10602

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52956 AN: 68006

Other (OTH) AF: 0.813 AC: 1718 AN: 2112

Alfa AF: 0.798 Hom.: 75235

Bravo AF: 0.821

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs4669887; hg19: chr2-12976179;