chr6-3057179-A-G

Position:

• chr6-3057179-A-G

Variant summary

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

The ENST00000433761.2(ENSG00000229282):​n.854A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,180 control chromosomes in the GnomAD database, including 45,353 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 0.77 (45353 hom., cov: 32)
• Consequence: ENST00000433761.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901242	XR_007059409.1	n.1618A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000433761.2	n.854A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116578 AN: 152060 Hom.: 45318 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.767 AC: 116664 AN: 152180 Hom.: 45353 Cov.: 32 AF XY: 0.766 AC XY: 56990 AN XY: 74404

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.738

Alfa AF: 0.817 Hom.: 101548

Bravo AF: 0.750

Asia WGS AF: 0.671 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7775816; hg19: chr6-3057413;