20-4425574-C-A

Position:

• chr20-4425574-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661308.1(ENSG00000236387):​n.283-2511G>T variant causes a intron, non coding transcript 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: ENST00000661308.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661308.1	n.283-2511G>T		intron_variant, non_coding_transcript_variant
	ENST00000661705.1	n.379-2511G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.372

Alfa AF: 0.409 Hom.: 18114

Bravo AF: 0.336

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485512; hg19: chr20-4406221;