rs6065912

Variant names:

• chr20-46003728-G-A
• rs6065912

Variant summary

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

The variant allele was found at a frequency of 0.122 in 152,182 control chromosomes in the GnomAD database, including 1,175 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 0.12 (1175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18531 AN: 152064 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.122 AC: 18542 AN: 152182 Hom.: 1175 Cov.: 32 AF XY: 0.122 AC XY: 9059 AN XY: 74414

African (AFR) AF: 0.112 AC: 4658 AN: 41514

American (AMR) AF: 0.0798 AC: 1220 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.0747 AC: 388 AN: 5192

South Asian (SAS) AF: 0.216 AC: 1041 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8839 AN: 67986

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.124 Hom.: 3065

Bravo AF: 0.116

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.55
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6065912; hg19: chr20-44632367;