rs235730

chr20-6755542-A-Gchr20-6755542-A-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 0.681 in 152,092 control chromosomes in the GnomAD database, including 36,393 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 0.68 (36393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 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: 0.681 AC: 103481 AN: 151974 Hom.: 36349 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.681 AC: 103581 AN: 152092 Hom.: 36393 Cov.: 32 AF XY: 0.682 AC XY: 50672 AN XY: 74352

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.696

Alfa AF: 0.612 Hom.: 30533

Bravo AF: 0.689

Asia WGS AF: 0.678 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235730; hg19: chr20-6736189;