rs6051841

Variant names:

• chr20-3412224-A-G
• rs6051841
• ENST00000773390.1:n.167+5518A>G

Variant summary

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

The ENST00000773390.1(ENSG00000288577):​n.167+5518A>G variant causes a intron change. The variant allele was found at a frequency of 0.197 in 152,244 control chromosomes in the GnomAD database, including 3,260 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 0.20 (3260 hom., cov: 33)
• Consequence: ENSG00000288577 ENST00000773390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.04
• Publications: 5 publications found

Genes affected

ENSG00000288577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773390.1. 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
	ENSG00000288577	ENST00000773390.1		n.167+5518A>G		intron	N/A
	ENSG00000288577	ENST00000773391.1		n.310+3448A>G		intron	N/A
	ENSG00000288577	ENST00000773392.1		n.335+3448A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30002 AN: 152126 Hom.: 3256 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.197 AC: 30007 AN: 152244 Hom.: 3260 Cov.: 33 AF XY: 0.192 AC XY: 14319 AN XY: 74444

African (AFR) AF: 0.255 AC: 10604 AN: 41536

American (AMR) AF: 0.182 AC: 2776 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.150 AC: 778 AN: 5182

South Asian (SAS) AF: 0.139 AC: 670 AN: 4826

European-Finnish (FIN) AF: 0.0925 AC: 982 AN: 10614

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12918 AN: 68002

Other (OTH) AF: 0.199 AC: 420 AN: 2112

Alfa AF: 0.189 Hom.: 1398

Bravo AF: 0.206

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.67
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs6051841; hg19: chr20-3392871;