rs4848143

Variant names:

• chr2-121054648-A-G
• rs4848143
• ENST00000785655.1:n.277-1739A>G

Variant summary

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

The ENST00000785655.1(ENSG00000302305):​n.277-1739A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,944 control chromosomes in the GnomAD database, including 23,653 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 0.51 (23653 hom., cov: 30)
• Consequence: ENSG00000302305 ENST00000785655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 publications found

Genes affected

ENSG00000302305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785655.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302305	ENST00000785655.1		n.277-1739A>G		intron	N/A
	ENSG00000302305	ENST00000785656.1		n.231-1806A>G		intron	N/A
	ENSG00000302305	ENST00000785657.1		n.230-1806A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77485 AN: 151826 Hom.: 23648 Cov.: 30

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.510 AC: 77487 AN: 151944 Hom.: 23653 Cov.: 30 AF XY: 0.511 AC XY: 37939 AN XY: 74250

African (AFR) AF: 0.159 AC: 6581 AN: 41472

American (AMR) AF: 0.575 AC: 8782 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2069 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2639 AN: 5142

South Asian (SAS) AF: 0.507 AC: 2431 AN: 4794

European-Finnish (FIN) AF: 0.654 AC: 6904 AN: 10556

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46114 AN: 67928

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.548 Hom.: 23646

Bravo AF: 0.487

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4848143;

hg19: chr2-121812224;