20-48592907-T-C

Variant names:

• chr20-48592907-T-C
• rs3924220
• ENST00000775767.1:n.132-17333A>G

Variant summary

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

The ENST00000775767.1(ENSG00000301042):​n.132-17333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,132 control chromosomes in the GnomAD database, including 4,216 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 0.23 (4216 hom., cov: 32)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 4 publications found

Genes affected

ENSG00000301042 (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 (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775767.1. 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
	ENSG00000301042	ENST00000775767.1		n.132-17333A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35399 AN: 152014 Hom.: 4200 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.233 AC: 35449 AN: 152132 Hom.: 4216 Cov.: 32 AF XY: 0.229 AC XY: 17034 AN XY: 74386

African (AFR) AF: 0.246 AC: 10212 AN: 41494

American (AMR) AF: 0.248 AC: 3789 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3470

East Asian (EAS) AF: 0.0966 AC: 500 AN: 5178

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2130 AN: 10592

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15854 AN: 67962

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.231 Hom.: 16466

Bravo AF: 0.233

Asia WGS AF: 0.159 AC: 553 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	0.58
DANN	Benign	0.61
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs3924220; hg19: chr20-47209445;