rs6071822

Variant names:

• chr20-39843516-G-A
• rs6071822

Your query was ambiguous. Multiple possible variants found:

• chr20-39843516-G-A
• chr20-39843516-G-T

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 0.186 in 152,118 control chromosomes in the GnomAD database, including 3,095 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 0.19 (3095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.186 AC: 28302 AN: 152000 Hom.: 3093 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.186 AC: 28316 AN: 152118 Hom.: 3095 Cov.: 32 AF XY: 0.189 AC XY: 14063 AN XY: 74364

African (AFR) AF: 0.0827 AC: 3434 AN: 41524

American (AMR) AF: 0.159 AC: 2428 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0898 AC: 311 AN: 3464

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5160

South Asian (SAS) AF: 0.183 AC: 880 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3460 AN: 10580

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16214 AN: 67972

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.212 Hom.: 11737

Bravo AF: 0.171

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.21
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6071822; hg19: chr20-38472158;