20-48574797-T-C

Variant names:

• chr20-48574797-T-C
• rs6012481
• ENST00000775767.1:n.249+660A>G

Variant summary

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

The ENST00000775767.1(ENSG00000301042):​n.249+660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,664 control chromosomes in the GnomAD database, including 41,058 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 0.73 (41058 hom., cov: 28)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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.249+660A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111133 AN: 151546 Hom.: 41001 Cov.: 28

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.734 AC: 111251 AN: 151664 Hom.: 41058 Cov.: 28 AF XY: 0.733 AC XY: 54278 AN XY: 74082

African (AFR) AF: 0.804 AC: 33235 AN: 41346

American (AMR) AF: 0.742 AC: 11298 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2475 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3192 AN: 5126

South Asian (SAS) AF: 0.608 AC: 2916 AN: 4794

European-Finnish (FIN) AF: 0.761 AC: 7984 AN: 10498

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47814 AN: 67890

Other (OTH) AF: 0.698 AC: 1473 AN: 2110

Alfa AF: 0.708 Hom.: 20923

Bravo AF: 0.738

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.44
DANN	Benign	0.63
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6012481;

hg19: chr20-47191335;