chr20-7128678-G-C

Variant names:

• chr20-7128678-G-C
• rs1473708
• ENST00000425900.1:n.82-17679G>C

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-17679G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,052 control chromosomes in the GnomAD database, including 1,436 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 0.11 (1436 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 1 publications found

Genes affected

ENSG00000232271 (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 (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232271	ENST00000425900.1	TSL:2	n.82-17679G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16061 AN: 151934 Hom.: 1438 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0935

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.106 AC: 16083 AN: 152052 Hom.: 1436 Cov.: 32 AF XY: 0.108 AC XY: 8049 AN XY: 74312

African (AFR) AF: 0.213 AC: 8819 AN: 41430

American (AMR) AF: 0.106 AC: 1616 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 324 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1569 AN: 5140

South Asian (SAS) AF: 0.157 AC: 758 AN: 4824

European-Finnish (FIN) AF: 0.0460 AC: 487 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2265 AN: 68008

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0146 Hom.: 8

Bravo AF: 0.114

Asia WGS AF: 0.248 AC: 865 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	0.078
DANN	Benign	0.45
PhyloP100		-0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1473708; hg19: chr20-7109325;