rs3096851

Variant names:

• chr2-203899159-A-C
• rs3096851
• ENST00000810800.1:n.203+2154A>C

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.203+2154A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,824 control chromosomes in the GnomAD database, including 10,952 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 0.37 (10952 hom., cov: 31)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 12 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810800.1. 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
	ENSG00000305408	ENST00000810800.1		n.203+2154A>C		intron	N/A
	ENSG00000305408	ENST00000810801.1		n.223+2154A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56244 AN: 151706 Hom.: 10940 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.371 AC: 56303 AN: 151824 Hom.: 10952 Cov.: 31 AF XY: 0.376 AC XY: 27923 AN XY: 74188

African (AFR) AF: 0.416 AC: 17211 AN: 41378

American (AMR) AF: 0.387 AC: 5907 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3028 AN: 5156

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4796

European-Finnish (FIN) AF: 0.489 AC: 5149 AN: 10526

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21963 AN: 67934

Other (OTH) AF: 0.320 AC: 674 AN: 2104

Alfa AF: 0.327 Hom.: 6449

Bravo AF: 0.369

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.63
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs3096851; hg19: chr2-204763882;