chr20-4321110-G-A

Variant names:

• chr20-4321110-G-A
• rs6076657
• ENST00000755410.1:n.51-18805G>A

Variant summary

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

The ENST00000755410.1(ENSG00000298420):​n.51-18805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,168 control chromosomes in the GnomAD database, including 4,475 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 0.19 (4475 hom., cov: 32)
• Consequence: ENSG00000298420 ENST00000755410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 0 publications found

Genes affected

ENSG00000298420 (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 = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755410.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298420	ENST00000755410.1		n.51-18805G>A		intron	N/A
	ENSG00000298420	ENST00000755411.1		n.555-18805G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29335 AN: 152050 Hom.: 4445 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.193 AC: 29409 AN: 152168 Hom.: 4475 Cov.: 32 AF XY: 0.189 AC XY: 14064 AN XY: 74402

African (AFR) AF: 0.422 AC: 17496 AN: 41478

American (AMR) AF: 0.125 AC: 1916 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5176

South Asian (SAS) AF: 0.192 AC: 925 AN: 4818

European-Finnish (FIN) AF: 0.0730 AC: 775 AN: 10614

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0964 AC: 6557 AN: 68002

Other (OTH) AF: 0.176 AC: 372 AN: 2110

Alfa AF: 0.119 Hom.: 2711

Bravo AF: 0.205

Asia WGS AF: 0.200 AC: 696 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	5.2
DANN	Benign	0.79
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6076657; hg19: chr20-4301757;