20-62440555-C-T

Variant names:

• chr20-62440555-C-T
• rs2427345
• ENST00000618678.3:n.390-6845C>T

Variant summary

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

The ENST00000618678.3(ENSG00000233017):​n.390-6845C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,104 control chromosomes in the GnomAD database, including 13,031 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 0.41 (13031 hom., cov: 33)
• Consequence: ENSG00000233017 ENST00000618678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 46 publications found

Genes affected

ENSG00000233017 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618678.3. 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
	ENSG00000233017	ENST00000618678.3	TSL:2	n.390-6845C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61905 AN: 151986 Hom.: 13020 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.407 AC: 61962 AN: 152104 Hom.: 13031 Cov.: 33 AF XY: 0.408 AC XY: 30369 AN XY: 74368

African (AFR) AF: 0.503 AC: 20843 AN: 41476

American (AMR) AF: 0.387 AC: 5923 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3468

East Asian (EAS) AF: 0.174 AC: 901 AN: 5184

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4337 AN: 10584

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25261 AN: 67964

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.382 Hom.: 38630

Bravo AF: 0.405

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		-2.5

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: rs2427345;

hg19: chr20-61015611;