3-3607616-C-A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.724

Alfa AF: 0.816 Hom.: 67442

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2129896; hg19: chr3-3649300;