20-7012982-T-C

Position:

• chr20-7012982-T-C

Variant summary

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

The variant allele was found at a frequency of 0.909 in 152,082 control chromosomes in the GnomAD database, including 63,728 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 0.91 (63728 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.974 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

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138117 AN: 151964 Hom.: 63688 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.909 AC: 138216 AN: 152082 Hom.: 63728 Cov.: 31 AF XY: 0.911 AC XY: 67713 AN XY: 74358

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.928

Alfa AF: 0.968 Hom.: 11718

Bravo AF: 0.901

Asia WGS AF: 0.963 AC: 3326 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038683; hg19: chr20-6993629;