6-34250941-T-C

Variant names:

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

Variant summary

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

The ENST00000586726.3(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 ENST00000586726.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 8 publications found

Genes affected

ENSG00000225339 (HGNC:58176):

ACMG classification

Our verdict: Benign. The variant received -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
SMIM29-AS1	NR_199000.1	n.103+2271T>C		intron_variant	Intron 1 of 2
SMIM29-AS1	NR_199001.1	n.103+2271T>C		intron_variant	Intron 1 of 1

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	ENST00000593917.4	n.151+2271T>C		intron_variant	Intron 1 of 1	3
ENSG00000225339	ENST00000659015.2	n.146+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

African (AFR) AF: 0.584 AC: 24116 AN: 41286

American (AMR) AF: 0.757 AC: 11533 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3201 AN: 3466

East Asian (EAS) AF: 0.874 AC: 4511 AN: 5164

South Asian (SAS) AF: 0.958 AC: 4604 AN: 4808

European-Finnish (FIN) AF: 0.980 AC: 10363 AN: 10572

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.966 AC: 65652 AN: 67990

Other (OTH) AF: 0.836 AC: 1761 AN: 2106

Alfa AF: 0.920 Hom.: 237984

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9394200; hg19: chr6-34218718;