20-48584971-A-G

Variant names:

• chr20-48584971-A-G
• rs6019300
• ENST00000775767.1:n.132-9397T>C

Variant summary

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

The ENST00000775767.1(ENSG00000301042):​n.132-9397T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,124 control chromosomes in the GnomAD database, including 26,827 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 0.57 (26827 hom., cov: 32)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.993
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.827 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301042	ENST00000775767.1		n.132-9397T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86594 AN: 152006 Hom.: 26771 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.570 AC: 86706 AN: 152124 Hom.: 26827 Cov.: 32 AF XY: 0.571 AC XY: 42448 AN XY: 74338

African (AFR) AF: 0.834 AC: 34647 AN: 41520

American (AMR) AF: 0.532 AC: 8141 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1848 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2546 AN: 5166

South Asian (SAS) AF: 0.626 AC: 3013 AN: 4812

European-Finnish (FIN) AF: 0.450 AC: 4754 AN: 10564

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29994 AN: 67980

Other (OTH) AF: 0.569 AC: 1201 AN: 2112

Alfa AF: 0.475 Hom.: 29635

Bravo AF: 0.583

Asia WGS AF: 0.614 AC: 2132 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	7.0
DANN	Benign	0.60
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs6019300; hg19: chr20-47201509;