chr6-151649219-A-G

Variant names:

• chr6-151649219-A-G
• rs3020310

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 0.201 in 151,934 control chromosomes in the GnomAD database, including 3,190 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 0.20 (3190 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30468 AN: 151816 Hom.: 3186 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.201 AC: 30491 AN: 151934 Hom.: 3190 Cov.: 30 AF XY: 0.197 AC XY: 14663 AN XY: 74256

African (AFR) AF: 0.207 AC: 8555 AN: 41400

American (AMR) AF: 0.159 AC: 2420 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3468

East Asian (EAS) AF: 0.0244 AC: 126 AN: 5154

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4808

European-Finnish (FIN) AF: 0.134 AC: 1419 AN: 10552

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15242 AN: 67968

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.211 Hom.: 2770

Bravo AF: 0.201

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.089
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs3020310; hg19: chr6-151970354;