ENST00000420000.6:n.200+18189T>G

Variant names:

• chr3-3608555-A-C
• rs9837561
• ENST00000420000.6:n.200+18189T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.200+18189T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,122 control chromosomes in the GnomAD database, including 2,240 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 0.14 (2240 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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+18189T>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20576 AN: 152006 Hom.: 2242 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.135 AC: 20600 AN: 152122 Hom.: 2240 Cov.: 32 AF XY: 0.130 AC XY: 9635 AN XY: 74380

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.0823

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.0459

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0914 Hom.: 1028

Bravo AF: 0.148

Asia WGS AF: 0.0460 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9837561; hg19: chr3-3650239;