rs4669887

Positions:

• chr2-12836053-T-G

Variant summary

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

The ENST00000663507.1(ENSG00000225649):​n.432+46106A>C variant causes a intron, non coding transcript 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: ENST00000663507.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663507.1	n.432+46106A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.813

Alfa AF: 0.800 Hom.: 11231

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669887; hg19: chr2-12976179;