chr20-4425574-C-A

Variant names:

• chr20-4425574-C-A
• rs10485512
• ENST00000661308.1:n.283-2511G>T

Variant summary

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

The ENST00000661308.1(ENSG00000236387):​n.283-2511G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,988 control chromosomes in the GnomAD database, including 10,569 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 0.35 (10569 hom., cov: 31)
• Consequence: ENSG00000236387 ENST00000661308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 8 publications found

Genes affected

ENSG00000236387 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661308.1. 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
	ENSG00000236387	ENST00000661308.1		n.283-2511G>T		intron	N/A
	ENSG00000236387	ENST00000661705.1		n.379-2511G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52897 AN: 151870 Hom.: 10562 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.348 AC: 52925 AN: 151988 Hom.: 10569 Cov.: 31 AF XY: 0.354 AC XY: 26266 AN XY: 74252

African (AFR) AF: 0.142 AC: 5880 AN: 41478

American (AMR) AF: 0.425 AC: 6489 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2191 AN: 5160

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4818

European-Finnish (FIN) AF: 0.523 AC: 5507 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28851 AN: 67942

Other (OTH) AF: 0.372 AC: 785 AN: 2112

Alfa AF: 0.400 Hom.: 24137

Bravo AF: 0.336

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.5
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10485512; hg19: chr20-4406221;