rs6069892

Variant names:

• chr20-56811695-T-C
• rs6069892
• ENST00000807007.1:n.283+32723T>C

Variant summary

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

The ENST00000807007.1(ENSG00000304895):​n.283+32723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,164 control chromosomes in the GnomAD database, including 10,015 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 0.33 (10015 hom., cov: 32)
• Consequence: ENSG00000304895 ENST00000807007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 4 publications found

Genes affected

ENSG00000304895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807007.1. 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
	ENSG00000304895	ENST00000807007.1		n.283+32723T>C		intron	N/A
	ENSG00000304895	ENST00000807008.1		n.254+32723T>C		intron	N/A
	ENSG00000304895	ENST00000807009.1		n.319+32723T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50546 AN: 152046 Hom.: 10019 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.332 AC: 50530 AN: 152164 Hom.: 10015 Cov.: 32 AF XY: 0.326 AC XY: 24281 AN XY: 74388

African (AFR) AF: 0.157 AC: 6519 AN: 41528

American (AMR) AF: 0.277 AC: 4234 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3472

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5182

South Asian (SAS) AF: 0.242 AC: 1169 AN: 4826

European-Finnish (FIN) AF: 0.448 AC: 4744 AN: 10578

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31479 AN: 67964

Other (OTH) AF: 0.339 AC: 716 AN: 2114

Alfa AF: 0.409 Hom.: 26391

Bravo AF: 0.312

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.23

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: rs6069892;

hg19: chr20-55386751;