chr20-39552181-C-A

Variant names:

• chr20-39552181-C-A
• rs2024791
• ENST00000774323.1:n.210-4609C>A

Variant summary

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

The ENST00000774323.1(ENSG00000300834):​n.210-4609C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,224 control chromosomes in the GnomAD database, including 337 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 0.056 (337 hom., cov: 32)
• Consequence: ENSG00000300834 ENST00000774323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906
• Publications: 0 publications found

Genes affected

ENSG00000300834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774323.1. 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
	ENSG00000300834	ENST00000774323.1		n.210-4609C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8449 AN: 152106 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0447

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

GnomAD4 genome AF: 0.0555 AC: 8452 AN: 152224 Hom.: 337 Cov.: 32 AF XY: 0.0599 AC XY: 4457 AN XY: 74412

African (AFR) AF: 0.0204 AC: 847 AN: 41554

American (AMR) AF: 0.0327 AC: 501 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.146 AC: 753 AN: 5148

South Asian (SAS) AF: 0.182 AC: 880 AN: 4824

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3918 AN: 68010

Other (OTH) AF: 0.0461 AC: 97 AN: 2104

Alfa AF: 0.0570 Hom.: 95

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.70
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs2024791; hg19: chr20-38180824;