chr3-143206165-G-A

Variant names:

• chr3-143206165-G-A
• rs6781977

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 0.642 in 151,948 control chromosomes in the GnomAD database, including 31,700 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 0.64 (31700 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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: 0.642 AC: 97494 AN: 151830 Hom.: 31671 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.642 AC: 97572 AN: 151948 Hom.: 31700 Cov.: 31 AF XY: 0.638 AC XY: 47340 AN XY: 74258

African (AFR) AF: 0.699 AC: 28965 AN: 41446

American (AMR) AF: 0.626 AC: 9557 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1851 AN: 3464

East Asian (EAS) AF: 0.568 AC: 2924 AN: 5152

South Asian (SAS) AF: 0.365 AC: 1757 AN: 4818

European-Finnish (FIN) AF: 0.667 AC: 7036 AN: 10552

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43394 AN: 67940

Other (OTH) AF: 0.623 AC: 1312 AN: 2106

Alfa AF: 0.627 Hom.: 16219

Bravo AF: 0.647

Asia WGS AF: 0.483 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.17
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6781977; hg19: chr3-142925007;