chr20-7113491-A-G

Position:

• chr20-7113491-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425900.1(ENSG00000232271):​n.82-32866A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,704 control chromosomes in the GnomAD database, including 17,372 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 0.44 (17372 hom., cov: 30)
• Consequence: ENST00000425900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000425900.1	n.82-32866A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65962 AN: 151590 Hom.: 17323 Cov.: 30

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.436 AC: 66069 AN: 151704 Hom.: 17372 Cov.: 30 AF XY: 0.431 AC XY: 31987 AN XY: 74130

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.421

Alfa AF: 0.354 Hom.: 1405

Bravo AF: 0.469

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232659; hg19: chr20-7094138;