rs6051846

Variant names:

• chr20-3423177-C-T
• rs6051846
• ENST00000773234.1:n.131-1099G>A

Variant summary

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

The ENST00000773234.1(ENSG00000300666):​n.131-1099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 149,640 control chromosomes in the GnomAD database, including 9,195 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 0.34 (9195 hom., cov: 30)
• Consequence: ENSG00000300666 ENST00000773234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 5 publications found

Genes affected

ENSG00000300666 (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 = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773234.1. 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
	ENSG00000300666	ENST00000773234.1		n.131-1099G>A		intron	N/A
	ENSG00000300666	ENST00000773235.1		n.284-6109G>A		intron	N/A
	ENSG00000300666	ENST00000773236.1		n.98-6109G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50129 AN: 149582 Hom.: 9186 Cov.: 30

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.335 AC: 50147 AN: 149640 Hom.: 9195 Cov.: 30 AF XY: 0.330 AC XY: 24049 AN XY: 72896

African (AFR) AF: 0.478 AC: 19461 AN: 40704

American (AMR) AF: 0.353 AC: 5239 AN: 14850

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1159 AN: 3456

East Asian (EAS) AF: 0.166 AC: 853 AN: 5124

South Asian (SAS) AF: 0.167 AC: 796 AN: 4778

European-Finnish (FIN) AF: 0.227 AC: 2237 AN: 9844

Middle Eastern (MID) AF: 0.230 AC: 65 AN: 282

European-Non Finnish (NFE) AF: 0.287 AC: 19434 AN: 67626

Other (OTH) AF: 0.327 AC: 676 AN: 2068

Alfa AF: 0.321 Hom.: 1408

Bravo AF: 0.351

Asia WGS AF: 0.171 AC: 595 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	1.1
DANN	Benign	0.34
PhyloP100		-0.082

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: rs6051846;

hg19: chr20-3403824;