rs6003959

Variant names:

• chr22-23922208-C-T
• rs6003959
• ENST00000703580.1:n.386+4236G>A

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.386+4236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,222 control chromosomes in the GnomAD database, including 3,333 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 0.19 (3333 hom., cov: 33)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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
ENSG00000290199	ENST00000703580.1	n.386+4236G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29317 AN: 152104 Hom.: 3325 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.193 AC: 29339 AN: 152222 Hom.: 3333 Cov.: 33 AF XY: 0.192 AC XY: 14281 AN XY: 74420

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.214

Alfa AF: 0.235 Hom.: 8932

Bravo AF: 0.187

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6003959; hg19: chr22-24264395;