20-18272302-A-G

Variant names:

• chr20-18272302-A-G
• rs761463
• ENST00000716728.1:n.244-1446T>C

Variant summary

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

The ENST00000716728.1(ENSG00000230010):​n.244-1446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,970 control chromosomes in the GnomAD database, including 29,268 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 0.61 (29268 hom., cov: 31)
• Consequence: ENSG00000230010 ENST00000716728.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 1 publications found

Genes affected

ENSG00000230010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716728.1. 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
	ENSG00000230010	ENST00000716728.1		n.244-1446T>C		intron	N/A
	ENSG00000230010	ENST00000716729.1		n.120-1446T>C		intron	N/A
	ENSG00000230010	ENST00000716730.1		n.371-1446T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93337 AN: 151852 Hom.: 29250 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.615 AC: 93410 AN: 151970 Hom.: 29268 Cov.: 31 AF XY: 0.609 AC XY: 45188 AN XY: 74236

African (AFR) AF: 0.711 AC: 29483 AN: 41440

American (AMR) AF: 0.558 AC: 8519 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2162 AN: 5170

South Asian (SAS) AF: 0.446 AC: 2148 AN: 4818

European-Finnish (FIN) AF: 0.585 AC: 6170 AN: 10542

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40757 AN: 67944

Other (OTH) AF: 0.600 AC: 1268 AN: 2112

Alfa AF: 0.612 Hom.: 3983

Bravo AF: 0.619

Asia WGS AF: 0.457 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs761463; hg19: chr20-18252946;