rs7270207

Positions:

• chr20-31733080-G-C
• chr20-31733080-G-T

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 0.0879 in 152,116 control chromosomes in the GnomAD database, including 663 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 0.088 (663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13344 AN: 151998 Hom.: 660 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0879 AC: 13378 AN: 152116 Hom.: 663 Cov.: 32 AF XY: 0.0852 AC XY: 6339 AN XY: 74382

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0268

Gnomad4 FIN AF: 0.0727

Gnomad4 NFE AF: 0.0764

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0100 Hom.: 3

Bravo AF: 0.0903

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7270207; hg19: chr20-30320883;