rs6901830

Variant names:

• chr6-33130567-G-A
• rs6901830
• ENST00000782892.1:n.430-10554G>A

Variant summary

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

The ENST00000782892.1(ENSG00000291111):​n.430-10554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,174 control chromosomes in the GnomAD database, including 1,473 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 0.13 (1473 hom., cov: 32)
• Consequence: ENSG00000291111 ENST00000782892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 11 publications found

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000301948 (HGNC:59163):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782892.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375021	NR_190905.1		n.*180C>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000782892.1		n.430-10554G>A		intron	N/A
	ENSG00000291111	ENST00000782893.1		n.404-10554G>A		intron	N/A
	ENSG00000291111	ENST00000782894.1		n.229-678G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19860 AN: 152056 Hom.: 1477 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.131 AC: 19870 AN: 152174 Hom.: 1473 Cov.: 32 AF XY: 0.130 AC XY: 9641 AN XY: 74386

African (AFR) AF: 0.0762 AC: 3164 AN: 41536

American (AMR) AF: 0.0951 AC: 1454 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3470

East Asian (EAS) AF: 0.134 AC: 691 AN: 5172

South Asian (SAS) AF: 0.148 AC: 711 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1866 AN: 10570

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11044 AN: 67990

Other (OTH) AF: 0.116 AC: 246 AN: 2114

Alfa AF: 0.148 Hom.: 3558

Bravo AF: 0.120

Asia WGS AF: 0.144 AC: 502 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	0.65
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6901830;

hg19: chr6-33098344;