rs6012418

Variant names:

• chr20-48407759-G-A
• rs6012418
• ENST00000615740.1:n.38+355G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-48407759-G-A
• chr20-48407759-G-T

Variant summary

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

The ENST00000655426.1(ENSG00000274261):​n.628+355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,204 control chromosomes in the GnomAD database, including 5,318 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 0.21 (5318 hom., cov: 33)
• Consequence: ENSG00000274261 ENST00000655426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 3 publications found

Genes affected

ENSG00000274261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655426.1. 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
	ENSG00000274261	ENST00000615740.1	TSL:5	n.38+355G>A		intron	N/A
	ENSG00000274261	ENST00000655426.1		n.628+355G>A		intron	N/A
	ENSG00000274261	ENST00000665877.1		n.576+355G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32335 AN: 152086 Hom.: 5291 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0894

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.213 AC: 32414 AN: 152204 Hom.: 5318 Cov.: 33 AF XY: 0.217 AC XY: 16123 AN XY: 74408

African (AFR) AF: 0.422 AC: 17491 AN: 41486

American (AMR) AF: 0.332 AC: 5071 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5186

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4832

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6077 AN: 68022

Other (OTH) AF: 0.183 AC: 386 AN: 2114

Alfa AF: 0.131 Hom.: 8554

Bravo AF: 0.241

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-0.41

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: rs6012418;

hg19: chr20-47036502;