20-680009-A-T

Variant names:

• chr20-680009-A-T
• rs7272428
• ENST00000755524.1:n.180-11594A>T

Variant summary

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

The ENST00000755524.1(ENSG00000298442):​n.180-11594A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,136 control chromosomes in the GnomAD database, including 6,656 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 0.28 (6656 hom., cov: 33)
• Consequence: ENSG00000298442 ENST00000755524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 0 publications found

Genes affected

ENSG00000298442 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755524.1. 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
	ENSG00000298442	ENST00000755524.1		n.180-11594A>T		intron	N/A
	ENSG00000298442	ENST00000755525.1		n.172-11632A>T		intron	N/A
	ENSG00000298442	ENST00000755526.1		n.172-7896A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42680 AN: 152018 Hom.: 6640 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.281 AC: 42740 AN: 152136 Hom.: 6656 Cov.: 33 AF XY: 0.273 AC XY: 20292 AN XY: 74382

African (AFR) AF: 0.403 AC: 16722 AN: 41480

American (AMR) AF: 0.242 AC: 3692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5188

South Asian (SAS) AF: 0.113 AC: 544 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2757 AN: 10570

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17407 AN: 68008

Other (OTH) AF: 0.268 AC: 565 AN: 2112

Alfa AF: 0.159 Hom.: 300

Bravo AF: 0.287

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		-0.12

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: rs7272428;

hg19: chr20-660653;