6-34250941-T-C

Variant names:

• chr6-34250941-T-C
• rs9394200
• ENST00000586726.3:n.136+2271T>C

Variant summary

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

The ENST00000593917.3(ENSG00000225339):​n.136+2271T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 151,824 control chromosomes in the GnomAD database, including 55,153 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 0.84 (55153 hom., cov: 29)
• Consequence: ENSG00000225339 ENST00000593917.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

ENSG00000225339 (HGNC:58176):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 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
ENSG00000225339	ENST00000586726.3	n.136+2271T>C		intron_variant	Intron 1 of 2	5
ENSG00000225339	ENST00000593917.3	n.136+2271T>C		intron_variant	Intron 1 of 1	3
ENSG00000225339	ENST00000659015.1	n.90+2271T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 126794 AN: 151706 Hom.: 55143 Cov.: 29

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.835 AC: 126841 AN: 151824 Hom.: 55153 Cov.: 29 AF XY: 0.837 AC XY: 62146 AN XY: 74236

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.836

Alfa AF: 0.943 Hom.: 104099

Bravo AF: 0.802

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.045
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9394200; hg19: chr6-34218718;