6-34250941-T-C

Position:

• chr6-34250941-T-C

Variant summary

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

The ENST00000586726.3(ENSG00000225339):​n.136+2271T>C variant causes a intron, non coding transcript 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: ENST00000586726.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586726.3	n.136+2271T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000593917.3	n.136+2271T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000659015.1	n.90+2271T>C		intron_variant, non_coding_transcript_variant

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;