6-11900673-G-A

Variant names:

• chr6-11900673-G-A
• rs6934027
• ENST00000848130.1:n.-167G>A

Variant summary

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

The ENST00000848130.1(ENSG00000310201):​n.-167G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 150,706 control chromosomes in the GnomAD database, including 61,161 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 0.90 (61161 hom., cov: 27)
• Consequence: ENSG00000310201 ENST00000848130.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 1 publications found

Genes affected

ENSG00000310201 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848130.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310201	ENST00000848130.1		n.-167G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.898 AC: 135169 AN: 150596 Hom.: 61121 Cov.: 27

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.897 AC: 135253 AN: 150706 Hom.: 61161 Cov.: 27 AF XY: 0.891 AC XY: 65512 AN XY: 73492

African (AFR) AF: 0.914 AC: 37562 AN: 41082

American (AMR) AF: 0.851 AC: 12904 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3173 AN: 3464

East Asian (EAS) AF: 0.632 AC: 3237 AN: 5120

South Asian (SAS) AF: 0.655 AC: 3133 AN: 4784

European-Finnish (FIN) AF: 0.937 AC: 9354 AN: 9982

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63032 AN: 67812

Other (OTH) AF: 0.891 AC: 1866 AN: 2094

Alfa AF: 0.892 Hom.: 5950

Bravo AF: 0.894

Asia WGS AF: 0.669 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.51
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6934027; hg19: chr6-11900906; COSMIC: COSV66714651;