rs6027755

Variant names:

• chr20-60693652-G-A
• rs6027755
• ENST00000789012.1:n.133+67C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-60693652-G-A
• chr20-60693652-G-C

Variant summary

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

The ENST00000789012.1(ENSG00000302709):​n.133+67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,052 control chromosomes in the GnomAD database, including 9,829 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 0.36 (9829 hom., cov: 32)
• Consequence: ENSG00000302709 ENST00000789012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 10 publications found

Genes affected

ENSG00000302709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789012.1. 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
	ENSG00000302709	ENST00000789012.1		n.133+67C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53920 AN: 151934 Hom.: 9811 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.355 AC: 54006 AN: 152052 Hom.: 9829 Cov.: 32 AF XY: 0.356 AC XY: 26468 AN XY: 74322

African (AFR) AF: 0.339 AC: 14055 AN: 41482

American (AMR) AF: 0.368 AC: 5623 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1344 AN: 3472

East Asian (EAS) AF: 0.150 AC: 773 AN: 5156

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4820

European-Finnish (FIN) AF: 0.341 AC: 3606 AN: 10582

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.372 AC: 25257 AN: 67958

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.361 Hom.: 37016

Bravo AF: 0.352

Asia WGS AF: 0.320 AC: 1118 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	2.1
DANN	Benign	0.49
PhyloP100		-0.39

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: rs6027755;

hg19: chr20-59268710;