rs1878321

Variant names:

• chr2-112786857-A-G
• rs1878321
• ENST00000762706.1:n.404+15961A>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+15961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,960 control chromosomes in the GnomAD database, including 8,221 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 0.32 (8221 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 8 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
	ENSG00000299339	ENST00000762706.1		n.404+15961A>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+15961A>G		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+15961A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48813 AN: 151842 Hom.: 8204 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.322 AC: 48874 AN: 151960 Hom.: 8221 Cov.: 31 AF XY: 0.321 AC XY: 23842 AN XY: 74280

African (AFR) AF: 0.407 AC: 16852 AN: 41392

American (AMR) AF: 0.293 AC: 4476 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.0793 AC: 411 AN: 5186

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4818

European-Finnish (FIN) AF: 0.315 AC: 3326 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20076 AN: 67948

Other (OTH) AF: 0.309 AC: 653 AN: 2110

Alfa AF: 0.327 Hom.: 1475

Bravo AF: 0.321

Asia WGS AF: 0.214 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.70

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: rs1878321;

hg19: chr2-113544434;