6-71733666-G-A

Variant names:

• chr6-71733666-G-A
• rs1204331
• ENST00000784456.1:n.131-10065G>A

Variant summary

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

The ENST00000784456.1(ENSG00000302111):​n.131-10065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,020 control chromosomes in the GnomAD database, including 36,583 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 0.69 (36583 hom., cov: 32)
• Consequence: ENSG00000302111 ENST00000784456.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 3 publications found

Genes affected

ENSG00000302111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784456.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302111	ENST00000784456.1		n.131-10065G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105116 AN: 151902 Hom.: 36560 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.692 AC: 105181 AN: 152020 Hom.: 36583 Cov.: 32 AF XY: 0.693 AC XY: 51514 AN XY: 74284

African (AFR) AF: 0.745 AC: 30893 AN: 41476

American (AMR) AF: 0.659 AC: 10067 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3229 AN: 5162

South Asian (SAS) AF: 0.733 AC: 3538 AN: 4824

European-Finnish (FIN) AF: 0.682 AC: 7191 AN: 10548

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45587 AN: 67964

Other (OTH) AF: 0.693 AC: 1454 AN: 2098

Alfa AF: 0.688 Hom.: 6096

Bravo AF: 0.686

Asia WGS AF: 0.663 AC: 2305 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.28
DANN	Benign	0.17
PhyloP100		-0.20

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: rs1204331;

hg19: chr6-72443369;