rs2129896

Variant names:

• chr3-3607616-C-A
• rs2129896
• ENST00000420000.6:n.200+19128G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-3607616-C-A
• chr3-3607616-C-G
• chr3-3607616-C-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+19128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,140 control chromosomes in the GnomAD database, including 40,130 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 0.69 (40130 hom., cov: 33)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 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
ENSG00000223727	ENST00000420000.6	n.200+19128G>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105025 AN: 152022 Hom.: 40110 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.691 AC: 105080 AN: 152140 Hom.: 40130 Cov.: 33 AF XY: 0.697 AC XY: 51845 AN XY: 74396

African (AFR) AF: 0.339 AC: 14044 AN: 41472

American (AMR) AF: 0.735 AC: 11240 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3884 AN: 5160

South Asian (SAS) AF: 0.828 AC: 3989 AN: 4818

European-Finnish (FIN) AF: 0.893 AC: 9483 AN: 10616

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57258 AN: 67998

Other (OTH) AF: 0.724 AC: 1532 AN: 2116

Alfa AF: 0.798 Hom.: 82981

Bravo AF: 0.660

Asia WGS AF: 0.764 AC: 2652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2129896; hg19: chr3-3649300;