rs6094710

Variant names:

• chr20-47466905-G-A
• rs6094710
• ENST00000814899.1:n.59-1973G>A

Variant summary

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

The ENST00000814899.1(ENSG00000306037):​n.59-1973G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,180 control chromosomes in the GnomAD database, including 224 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 0.049 (224 hom., cov: 31)
• Consequence: ENSG00000306037 ENST00000814899.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 25 publications found

Genes affected

ENSG00000306037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814899.1. 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
	ENSG00000306037	ENST00000814899.1		n.59-1973G>A		intron	N/A
	ENSG00000306037	ENST00000814900.1		n.58+13554G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7461 AN: 152062 Hom.: 225 Cov.: 31

Gnomad AFR AF: 0.0688

Gnomad AMI AF: 0.0848

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0490 AC: 7459 AN: 152180 Hom.: 224 Cov.: 31 AF XY: 0.0474 AC XY: 3527 AN XY: 74408

African (AFR) AF: 0.0686 AC: 2849 AN: 41524

American (AMR) AF: 0.0480 AC: 732 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4822

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3089 AN: 68006

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0512 Hom.: 209

Bravo AF: 0.0516

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.65
PhyloP100		-0.80

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: rs6094710;

hg19: chr20-46095649;